Help from Unexpected Places
by Wild Force Ranger
Summary: Ever since John Sheppard stepped onto Atlantis, the city's been waking. Now he's woken something he can't shut off...Gen. Chap 23: Snippet to test new style.
1. 38 Minutes: Suspicion

This is--hopefully--the start of a series...I'm planning on going through the whole show right up to current episodes. Let me know what you think.

Disclaimer: I own none of these. Except...well, not telling, that would spoil it. But I own very little of what's here...even most of the words aren't mine.

Warning: If you don't remember these episodes, you may be a little confused at times.

38 Minutes

Later, when he thought about, John realised he was lucky it had started when it did. The first couple of times his teammates put it down to the medication he was on. And after…

Well, after it didn't matter so much.

Teyla was sitting by his bed in the infirmary, passing along well wishes from the Athosian children, when John saw a young girl peering around the doorframe. Unusually, she was blonde; he didn't think he'd seen a blonde Athosian yet.

"Ask her in, Teyla," he suggested.

"Ask who?" She followed his gaze to the door. "No one is there, John."

"One of the kids was there. A little blonde girl."

Teyla eyed him. "There are no blonde girls among the children, John. Are you feeling well?"

"Yeah. I'm…just tired, I guess."

"Perhaps you should get some rest."

John smiled, idly wondering how Teyla managed to imply 'you idiot' while apparently being totally sincere. "Sounds like a plan," he agreed. "Wake me if anything good happens."

"I shall. Sleep well."

He really was tired. Turned out having the life drained out of you was really draining…who knew? Sighing, he settled down to sleep.

* * *

The next time he woke up the girl was sitting cross-legged on the end of his bed, studying him. "You _do_ see me," she said delightedly. "I thought you did, and then Teyla didn't so I was sure…" 

She slid off the bed, and some part of him noted the weight on the mattress didn't shift.

"Everything's going to be different now," she said wisely, looking up at him.

"What's going to change? Hey! Who are you?"

Dr Beckett rounded the privacy screen, talking over his shoulder to someone. The girl slid neatly under his arm and vanished. "…soon, all right? Thank you, lass. Major! Are you talking to someone?"

"Just myself, apparently. So what's the good word, Doc? Can I get out of here or what?"

"Well, I'm a little worried about this new habit of talking to yourself," Carson said. He kept a straight face for almost two seconds…a personal best…before giving up.

"That's it. I'm out of here."

"Aye, you can go," Carson agreed. "Light duty only! No Gate travel."

"Aw, Doc.."

"No. Light duty for another three days. Come back to me then. And Major? If you start answering yourself, come see me."

"Very funny, Doc. Thanks."

Suspicion

After that John caught fleeting glimpse of her around the city. No one else seemed to see her; after the first couple of times he tried to point her out to people he gave up.

He'd decided he wasn't imagining her; with all the weird things in his head, he thought if he ever did start imagining things, a little blonde girl in the uniform of the Ancients and—of all things—an Alice band probably wouldn't be the first thing to appear.

It did startle him slightly when he walked into the conference room to find her sitting on the table, swinging her legs. "Hi!" she said brightly.

"Excuse me? Who are you?"

"Atlantis," she said, as though it should have been obvious. Then, shrugging, she added, "Well, bits of Atlantis, anyway."

"What bits?"

She leaned to one side, almost falling off the table. "You know your people can see you, right?"

"What?"

"And they can't see me? I thought you'd figured that out by now."

John took a deep breath, sitting carefully at the table so his face couldn't be seen. "What parts of Atlantis?"

"Better. We don't want your friends to think you're insane."

"What bits of Atlantis?"

"Memory banks and sensors. Mostly." She smiled, starting to swing her legs again. "I'm designed to facilitate information gathering and problem solving."

"Designed?"

She nodded brightly. "I'm holographic…more or less. A representation. Like the woman down in the map room."

"The woman down in the map room is a _woman_. And you're…" He gestured vaguely, trying to make it look like a stretch.

"I'm supposed to look sufficiently different from your peers that you can pick me out. The children are in a minority here, and none of them are blonde."

"Nice choice. Look…"

The door hissed open and he turned, rising as Rodney and Elizabeth came in. Bates was trailing behind them.

From the corner of his eye, he saw the girl rise to her feet, wandering idly across the top of the table until she reached the unoccupied side. Bouncing to ground level, she leaned against the table, arms folded.

"You should listen to Rodney," she prompted him, and he jerked his attention back.

"…on certain planets that pick up the transmission and then alert the nearest Hive Ship. Those were the planets where we were attacked."

"Boy, do we owe a few people an apology," John said pointedly. Bates shifted, but he didn't answer.

"Teyla had no idea she was giving away your position?" Elizabeth asked. John shifted; the girl was sliding along the table, eyeing Teyla's locket curiously.

"She said it was a present from her father. She lost it when she was a kid." John was only half paying attention; even knowing the kid was invisible or intangible or whatever, it made him itch seeing her standing so close to Elizabeth.

"It's pretty," the girl said indifferently, backing away. "Especially for a Wraith. No sense of aesthetics, those things."

"So some Athosian thought this would make a nice little necklace?"

He'd been speaking to her and was surprised when Rodney answered. "What am I, Answer Man? The point is…"

"It wasn't Teyla," Elizabeth interrupted him. "Or any other Athosian, for that matter."

"If that's the case…" John smiled. "We can use it against 'em."

* * *

The Wraith looked up when John came into the holding area. "Again…Your kind is persistent. I would have thought you'd given up by now." 

"Aww, hell, I've got all the time in the world. Now you on the other hand…"

The Wraith tried to grab him through the bars; John jerked backwards, and the forcefield flared to life between the bars, blocking the Wraith in.

The girl was standing on the other side of the cell when John recovered, glaring at the prisoner.

"The ancients were pretty good at shields and stuff like that weren't they," John continued easily. "I give you a week. Maybe two…tops."

"You waste your time," the Wraith told him. "I'll provide you with no information."

"Wonder what hurts more, the gun shot wound or the hunger? Because I'd love to help out but…how did McKay put it?" His voice hardened. "We can't meet your dietary requirements."

"When I am free you will be the first that I feed upon," the Wraith promised him.

"Okie dokie…I'm going to go make myself a sandwich." He turned as if to leave, pausing when the Wraith spoke again.

"Human. You think you've won a victory by my capture but by bringing me here you've only hastened your own doom. It's only a matter of time before the others of my kind come to rescue me…and when they do…They'll be no where in this world you can hide."

"Stay positive now," John warned him, leaving.

* * *

The girl was leaning against the wall outside; she fell into step with him, waiting patiently until they reached the transporter. "You shouldn't keep him here," she warned him. 

"Yeah, I've heard that," he agreed vaguely. "Why can't anyone else see you?"

"They're not of the People. Not the way you are."

"The People?" He could hear the capital P when she said it.

She gestured around them. "The People who lived here."

"The Ancie—the gene. Is that it? I have the gene and they don't?"

"A gene," she repeated slowly. "Yes…yes, your doctor's been researching that. The gene would explain it."

John came to a halt; she overshot him, turning back to stare at him quizzically.

"Why," he said slowly, "can't anyone see you?"

"Because they're not in tune with the city the way you are. I'm in your head, John, projected in there. You don't see or hear anything."

John thought about that. "Oddly, that's not the most insane thing I've heard today."

"There are records of it happening before in your own computers. Your SIGI…"

"SG1," he corrected her.

"…team encountered a being called Urgo. They saw and heard him, but he wasn't really there."

"That's reassuring," John muttered. "Why didn't you show up as soon as we got here?"

"The city was locked down. Everything…including me…was turned off when the People left. When your people started powering up they were concentrating on essential systems, and I'm not counted as essential." She made a face at her own statement.

"Information retrieval? Can't think why. Especially since no one can see you."

"Everyone could see me. Your people aren't People, they can't see me."

"Other people have the gene," he pointed out.

"Not strongly enough. Towards the end of the War there were People who couldn't see me." She shrugged, looking back down the corridor. "I'm not made to understand things, just to retrieve information. I can quote you anything you like from the memory banks."

"Ours or yours?"

"Either." She grinned. "Dr McKay has some very interesting hidden files in his system. Would you like me to tell you?"

"Please don't." John started towards his quarters again.

"Why is Samantha Carter so hot? Is she ill?" The girl trailed behind him.

"Really. Please don't."

"How hot do you have to be before you start smoking?"

"Stop now."

He managed to close the door in her face, but when he turned she was sitting on the edge of his bed. "I'm _Atlantis_, remember? I'm everywhere." She grinned.

John sighed. "What are the chances I'm dreaming all this?"

"Slim to none. Tell me, why is…"

"Alice!" he interrupted her.

"Atlantis."

"You look more like an Alice to me. Look, if McKay's encrypting stuff it's probably for a good reason, so leave it alone. And if you don't mind? I'd really like some privacy."

"Fair enough," she agreed easily. "Just in here, or somewhere else as well?"

"In here," he said warily.

"Good." She grinned again. "See you in the morning." Between one heartbeat and the next she was gone.

John grimaced, wiping his eyes. "This is gonna be interesting."


	2. The Storm

Hi guys! Welcome to The Storm.

MuseUrania, Bokorman, and Titan5, thanks for the reviews! Those of you who didn't review, but did put me on alert, thanks for that too. Enjoy this chapter.

The Storm

"Haven't been to the mainland in a while. How's everybody settling in?" John asked absently.

"Halling believes the first crops will have a good yield," Teyla told him.

"You still miss home?"

"There is still talk of returning, even though I've told them the Wraith have scorched Athos bare in revenge for our resistance."

"Well, maybe in time this place will start to begin to feel like home."

Half John's attention was on Alice, standing between the two seats. The 'Jumpers, he'd discovered, had their own versions of the Alice program; less well informed than the Atlantis version, but just as willing to answer questions. The programs all updated each other after any separation; John was getting used to having Alice give him mission reports as soon as the 'jumpers came home.

She could also gain limited information from the lifesigns detector; John already carried his on all his missions, but he made sure any team with a gene-empowered member carried one at all times as well.

"John," Alice said warningly, just as Teyla said "Do you see that?"

"That _can't_ be a storm," John said slowly. "It stretches across the whole horizon."

"It is. I know that storm, John. It..."

Alice cut herself off when Teyla said thoughtfully "I've never seen something like that from so high."

"I've seen a lot of things from this altitude, but nothing like that." He reached for the comm, flicking it on. "Atlantis base, this is Jumper One. We're gonna change our heading to investigate a storm."

"_Major, this is Weir. We didn't...at. You're break...up."_

"They won't hear you," Alice murmured. "Those storms put out too much interference."

John repeated the message patiently; Weir acknowledged it, signing off.

John lifted the 'Jumper higher, studying the mass of cloud uneasily.

"Do all storms look like this from above?" Teyla asked.

"We should go home," Alice said quietly.

"No," John told both of them. "This must cover twenty percent of the planet."

"Is it headed towards the mainland?" Teyla asked, studying the display.

"Tracking right towards the settlement," John agreed grimly.

"And after that?"

John deliberately didn't look at Alice. "Straight to Atlantis."

* * *

"This planet is basically the same size as Earth. Now, hurricanes on Earth never get as big as this bad boy because once they hit the shore, the brakes get put on. Without as much landmass to slow it down here, it's just, uh, gaining momentum." McKay, as usual, was talking with his hands.

_"Both_ of them are," Zeenka said pointedly.

"Yes," McKay agreed.

"_Both_ of them?" Elizabeth repeated sharply.

"We saw only one," Teyla protested.

"It only _looked_ like one," McKay said dismissively. "Now, according to the Ancient database, every twenty or thirty years the sea gets unseasonably warm. Now that, for reasons too boring to get into, means that hurricanes are much more likely to occur."

John tuned the pair out; Alice was standing at the door, staring at the wall behind Elizabeth as though she could see the storm. Voice flatter than he'd ever heard, she said quietly, "The storms come every twenty six years. Nothing stands against them. It's why the People never built on the mainland." She glanced up, catching John's eye. "The city will drown."

Echoing her disconcertingly, Elizabeth said, "You just said the Ancients experienced these storms every twenty to thirty years. Atlantis must have some sort of precautions put in place."

"In the past, the Ancients have been protected by the shield or submerged deep enough in the water not to be affected."

"OK – strike those options. What else have we got?" John asked. Zelenka shrugged helplessly, Rodney looked away, and Alice didn't react to the question at all.

"Nothing," Zelenka said quietly. "It is a real threat. The high winds alone will wreak havoc."

"C'mon, guys!" John protested. "This city's been around for a long time."

"With no shield and no way to submerge, the city hasn't a chance of surviving." Alice looked away, at the wall, again. "I can give you odds."

"This is _Atlantis_! I mean, they've gotta be able to handle that ... right?" John looked to McKay.

"No."

"Why _not_?" Elizabeth demanded.

"The people who built this city knew they had a forcefield capable of holding back anything Mother Nature or, for that matter, the Wraith could throw at them. Without that protection, Atlantis is remarkably fragile."

"There was no need for any other way," Alice agreed. "The shield protected them. It always protected them."

"Flooding could sink the city entirely," McKay added.

"How could something as big as Atlantis just...sink?" Ford asked helplessly.

"I'm sure the passengers on the Titanic were asking themselves the same question," John muttered.

"Yes, well let's not!" McKay said quickly.

"So what you're saying is," John said slowly, "if Teyla and I hadn't discovered this, we ..."

"We would be in even bigger trouble," Elizabeth finished. "Alright, what's the plan?"

McKay glanced at his watch. "By my calculations we have just under, what, twelve hours until the storm hits, so, uh, we plan to _have_ a plan ..."

"Yeah," Zelenka agreed.

"... by then," McKay finished.

* * *

Alice was already in the lab when John led Ford in; she was sitting on the edge of a table, watching with some amusement the argument between McKay and Zelenka.

"He's on the right track," she said, gesturing to Zelenka. "McKay's just not giving him the time to think about it."

"Well, I got a green light from Smeadon and the Manarians," John said, mostly to McKay. "I'm not sure how pleased he'll be if we get stuck there, though. That's not gonna happen, though, right?"

"Of course it's not," McKay said immediately. "We can always gate off to another planet."

"Comforting! Thank you!"

"Are we sure there's no part of the mainland we could go to?" Ford asked.

Elizabeth and Teyla came in in time to hear the question, and Teyla answered "Everywhere that we've explored is in the path of the storm. My people are evacuating even now."

"Still, Ford's right," John said thoughtfully. "I mean, the mainland's the size of North America. You're telling me the entire continent's gonna get hit? It's just I'd rather not owe Smeadon any favors."

Alice was shaking her head, but she didn't speak.

"If we lose Atlantis we'll be stuck on the mainland without any access to the Stargate," Elizabeth reminded him.

"Well, McKay will come up with something."

"I will _try_, but despite what you all may think, I am not Superman."

John glanced around the room. "Was anyone seriously thinking that?"

Elizabeth shook her head, almost smiling. Another scientist agreed, and John glanced at Ford.

"No, sir."

"Never," Zelenka agreed emphatically.

"Fine!" McKay huffed. "My point is, the storm will affect over seventy percent of the mainland, and Atlantis isn't safe either. If you want everyone to live, you gate them offworld."

"Abandon Atlantis?" John repeated.

"_No,_" Elizabeth said quickly. "We're coming back, John."

He nodded slowly, watching Alice watch him. "We're coming back," he agreed.

* * *

It took a long time to organize the whole evacuation. John restricted everyone's luggage, refused any requests to take tech, and only allowed weapons to the guards. It still took a ridiculous amount of time to get everyone sorted out and through.

Finally he got the last group through; as the 'Gate shut down he ordered the last two guards, "Evacuate the people on inbound Jumper Two as soon as they come in."

"Yes, sir."

John glanced up as Alice stepped in from the corridor, gesturing at him. Nodding to the guards, he followed her out into the corridor, trailing Elizabeth and McKay but too far behind for them to hear.

"What is it?" he asked quietly.

"They have an answer. McKay and Zelenka found a way to save the city."

"It'll work?" he asked warily.

"It should, if it happens just the way they think."

"No margin?"

"Very little. My city wasn't built to do what they're asking of her. If it fails, she'll burn while she drowns."

"McKay's almost as smart as he thinks he is. If there's a way to make it work, he'll find it."

Alice nodded quietly, vanishing midstep, and he quickened his pace to catch up with the others.

* * *

"There are dozens, possibly hundreds of lightning rods placed strategically around the city," McKay started.

"Wait a second," John protested.

"What?"

"Why?"

"Why what?"

"Why are there hundreds of lightning rods placed around the city? Wouldn't the shield protect against lightning?"

McKay nodded quickly. "Yes, yes, it would, but running the shield all the time is only good for one thing – draining power."

"Right..."

"You're aware that there's a time element to what we're doing here, right?" he demanded.

"Yes, it's been brought to my attention," John agreed.

"Like I was saying, there are lightning rods – a lot of them – placed all over the city. Now, as it stands right now, all the energy they capture is routed into four main grounding stations. In turn the stations ground all that energy into the ocean below."

"So instead of sending all that energy to ground ..." John trailed off.

"... we use it to power the shield," McKay finished triumphantly.

"How?" Elizabeth asked.

"By directing it right down the corridors of Atlantis and into the shield generators."

"The city can handle that?"

"Yes – theoretically," McKay said carefully.

Alice reappeared, nodding in McKay's direction: John chose to take that as confirmation of the theory. "Like dinosaurs turned into birds theoretically, or theory of relativity theoretically?" he asked anyway.

"What? Uh, sort of between. Elizabeth – you take grounding station two; I'll take grounding station one; Major – you take stations three and four."

"Woah, woah, wait a second – where _are_ stations three and four?"

McKay turned to a map on one of the walls; the stations at the outer edge of the city were flashing, and John was sure they hadn't been a minute ago. McKay didn't notice, or didn't think it worth worrying about, because he simply pointed. "Here, and here."

"And we are ...?"

Another point began to flash, this time near the center of the city; John glanced irritatedly at Alice, who only smiled innocently.

McKay started talking faster, which usually meant he was nervous about something. "Here, yes. I need to get done quickly so I can start working on the subroutines, and Elizabeth was complaining about her knee the other day ..."

"Wait, wait, wait a second. Are these things even close to a transporter?"

"Uh, yes, Elizabeth's is."

"And _mine_?" John demanded.

"Uh, it's a brisk walk away."

"And by 'brisk', you mean ... 'far'."

"By 'walk', I mean 'run'," McKay agreed.

John sighed. "OK."

"You need to radio in once you've got to your first station."

"Alright. Let's do it," he agreed, gesturing for Alice to follow him as he left at a jog.

* * *

The edge of the storm had already hit; John stared at the wind for a moment before opening the door. The grounding stations were all outside, and the balcony offered no protection.

He lifted one hand to his radio, fighting the wind. "I'm here!"

"_I told you to contact me when you got to the first one, Major_," McKay said.

"I _am_ at the first one, Rodney!"

"_Oh, sorry. I've already done mine."_

John rolled his eyes for Alice's benefit. "That's great! Good for you!"

Elizabeth's voice added, _"Me too._"

"Good for everyone!" John snarled.

"_Where are you now?"_

"I'm at the damned grounding station!"

"_No, no, no, no, not you."_

"_I'm in the transporter,_" Elizabeth told him.

"_There you are."_

"_There I am_," she agreed.

"Glad everybody's having such a good time. What do I do?"

"There should be a keypad right on the console of the station." Alice pointed, illustrating Rodney's narration as he described how to turn off the grounding station.

"_That do it?"_ he asked.

The grounding rod split open along its' length, and John nodded. "Yeah!"

"_Good. Three down, one to go. They all seem to have the same separation code, so get to the next one, repeat the procedure. We'll meet you in the Control Room."_

"Roger that." John headed back inside, pausing for a moment to catch his breath.

* * *

He was halfway to the grounding station when his radio crackled.

"_Apparently there's wounded incoming," _Elizabeth warned him.

"Doesn't make any sense. They said it was Wraith-related?" John stopped running, not willing to risk missing her answer.

"_We'll ask them ourselves in a second – hold on...What the hell is going on?"_

John wrapped one hand around his mic, hissing "Alice!" She stepped out of the nearest doorway, and he demanded "What's happening in the 'Gate room?"

Her eyes went distant for a moment. "You've been invaded."

"I..." Gesturing her to follow, he started running again. Elizabeth had left her radio on; he could hear snatches of the conversation, enough to grasp the basics of the situation.

Alice didn't bother trying to keep up with him, but when he reached the 'Jumper bay she was standing outside 'Jumper One. The 'Jumper version of her was nowhere in sight, which was probably just as well. Two Alices had a habit of either speaking in tandem or finishing each other's sentences, and John really didn't want to deal with that right now.

"I need the lifesigns dectector," he told her, stepping past. The lights flicked on and the detector slid out of its' compartment. John picked it up in one hand, turning on the comms with the other. "Jumper Two, this is Sheppard, come in. ... Jumper Two, do you copy?"

"_This is Ford, sir. We decided to wait out the storm in the Jumper."_

"You're still on the mainland?"

"_Yes, sir._"

"We've got a situation here. From what I can ascertain, a small Genii strike force has gated in."

"_The Genii?!"_ Ford repeated._ "The folks who wanted us to build them an A-bomb?"_

"Yeah, that's them, and they've got Weir and McKay hostage. They've also got control of the Gateroom."

"_You're breaking up, sir – did you say hostage?_"

"Affirmative."

He faintly heard Beckett swear in the background before Ford said, "_We're on our way._"

Ford had some kind of argument with Beckett and Teyla, too low-pitched for John to make out; he turned on the lifesigns detector, watching the little dots wander around the 'Gate room.

"_Major, this is Teyla. The hurricane is in full force outside. We could attempt to fly through it but it is doubtful that we could make it back to Atlantis; and we have three young passengers._"

"That's bad news."

"_I'm sorry_," Teyla offered.

"So am I. Just stay put til it passes over."

"_Sir..._" Ford protested.

"It's OK, Lieutenant. Just get your ass back here as soon as you can. I could use a little back-up."

"_Good luck, sir."_

* * *

John hesitated when his radio flipped on again; Rodney was talking quickly, urgently, but the sound was muffled by distance.

"Supplies?" he murmured to Alice.

"C4, medical supplies, the Wraith data tablet," she repeated easily. The radio cut out again, but she continued. "The Genii Commander is sending Weir with some men to begin collecting the supplies, and he is asking McKay about the plan to save the city."

"Where are the Genii going?"

Alice looked away. "The lab, for the Wraith tablet."

John nodded, glancing down at the detector. "All right. Stick around."

"Never far away."

* * *

Alice stopped mid-step. "They've found the empty armory. John?"

"What?" John was studying the detector.

"They know about the plan. The lightning."

"How do they know about the plan?"

"The leader hurt Rodney. He's all right," she added, fast. "Scared. Not hurt badly. But he told him about the grounding stations."

John started to answer, but his radio crackled to life. "_This is Commander Kolya."_

"Kolya," John repeated. "That's a hard name to pronounce. Is that a first name? My name's Major John Sheppard and I have hidden the C4 where you will never – I repeat, never – find it. When I get confirmation that the prisoners have been safely released and allowed to gate off Atlantis, I will help you find it."

"_Your offer is very generous, Major."_

"Yes, it is."

"_However, Doctor McKay recently shared with me there's a plan in action to save the city."_

"He _did_" John repeated, eyeing Alice.

"_He did. My understanding is there is one final grounding station that needs to be deactivated. Uncouple the grounding rods at Station Three, assist with the reactivation of the shield, and you and your friends can leave here unharmed._"

"Wait a minute – I thought all you wanted was C4 and a Jumper."

He figured it out at the same moment Kolya said it. _"Why raid a city when you can seize it, Major? Atlantis will be ours or the ocean's. You choose."_

* * *

John studied the detector, frowning. "They're surrounding the grounding station."

"They are," Alice agreed.

John backed towards the wall, eyes on the screen. "What are they doing?"

"One's coming in. Door..."

John shot the man almost before he was inside, backing towards the window.

"Another. Three, two..."

He ducked on Alice's 'one', hearing the console explode behind him. As soon as he hit the ground he shoved back up, shooting the solider as he tried to reload.

Alice was standing over the console, grimacing. "Fried," she said briefly. John snatched a communicator from one of the bodies, coming to join her.

"Let me tell you what you did wrong here, Kolya," he told the device. "A: you lost two of your men. B: you damaged the switch before I could separate the grounding rods, which I'm sure you're gonna get an earful from McKay for; and C: you lost all of what little credibility you had with me."

"_You killed two of my men,"_ Kolya said after a moment.

"I guess we're even!"

"_I don't __like__ even."_

"John, he's got a weapon," Alice hissed.

"I'm not finished yet!" John said quickly.

"_Neither am I. Say goodbye to Doctor Weir."_

John looked at Alice, who shook her head helplessly. "The city has a self-destruct button," he warned the Genii. "You hurt her, I'll activate it. Nobody'll get Atlantis."

"_Even if it exists, Major, you need at least two senior personnel to activate it – and I'm about to take one of them out of the equation."_

"Kolya?! Kolya?! I'll give you a ship! I'll fly it out of here for you myself! _KOLYA_!!"

A shot echoed over the connection.


	3. The Eye

Hey Titan5 and faldo, thanks for the reviews. Don't worry, faldo, John is still super--Alice can't really affect anything, only give him information.

The Eye

"Kolya!!" John yelled again. A shot echoed over the communicator; he flinched, looking at Alice, who shook her head quickly. "Kolya! Don't do this!!"

The communicator was silent for a long time; Alice studied the console intently, finally shaking her head. "McKay may be able to fix it. We can't."

"You don't know how?" John said dully.

"I know the schematics. I'm not built for repairs. And I don't know the English terms for the..." She gestured vaguely. "Parts. Components."

"They ok?"

"They're fine. Scared. That's all." She hesitated briefly. "Kolya was going to hurt Weir, I think. McKay talked him down. They're both fine."

The communicator crackled back to life. "Major Sheppard…How's this for credibility? Weir is dead."

John took a deep breath before answering. "I. Am. Going. To. Kill. You."

"Maybe," Kolya agreed, eerily disinterested in the possibility. "Stay out of my way. Or Mckay will join her."

John took another, very deep breath before turning and heading out of the grounding station.

* * *

John slowed, staring at his palm scanner. On the level below him, three Genii were inching along. John's communicator was still picking up their chatter; another Genii, Ladon, was guiding them from the control room. 

"Where did he go?" one of the soldiers complained. The words echoed oddly, filtering up through the grate under his feet and coming over the communicator as well.

"_Shh_," Ladon said irritably, "_he can probably hear your stupid questions_."

John pulled two smoke grenades from his pocket, pitched them over the edge of the rail and hurried on quickly, setting off more grenades as he went.

"_20 feet away…_" Ladon said patiently. "_5 feet..."_

"_There's so much smoke…._" the soldier protested. _"Which way?"_

"_You're right on top of him!"_

"_Yeah? I think I would see him if I was."_

John glowered down at them from the walkway above.

* * *

Alice was waiting when he turned away. "Kolya knows you're killing his men. He's called them back to the control room, and he's sending for reinforcements." 

"Let him," John said, brushing past her. "How are they?"

"They're fine. McKay almost has the grounding station fixed. They're planning how to stall."

"Good. Good for them. Okay, what would McKay do?" He headed away down the corridor again.

Alice considered McKay's handwritten sign. "Really Really Dangerous Don't Touch McKay," she read. "Who would want to touch McKay?"

"Well, if you listen to gossip..." John said absently. "You know why we're here?"

"You want to blow the reactor, cut Kolya's power."

"Yeah." He studied her. "What about you?"

"My program's not run from this generator. Go ahead...pull this."

He gripped the part she pointed out, yanking it from the casing. Alice flickered, so briefly he thought he'd imagined it.

"Control room's down, most of the secondaries are down," she reported. "You're making them very unhappy."

"Good. Elizabeth and McKay?"

"They're fine...I'd tell you, you know."

"You didn't tell me when he got hurt!"

"We were a little busy at the time, I'd just been invaded!" She glanced away. "One of them's suggesting guarding the generators. Kolya's refusing."

"Good. That makes it easier."

* * *

The next generator cut the power to the grounding station. Alice listened for a moment before reporting that Kolya had capitulated and was sending men to all the generators, to attempt to fix the ones he'd damaged and protect the ones he hadn't reached yet. 

"They're expecting the reinforcements soon," she added. "John..."

"What?"

"Jumper Two just docked. Ford, Teyla and Beckett are heading for the armory."

"Just them?"

"There are three Athosians in the 'Jumper, but they've been told to stay there. Beckett has the detector, they're watching out for you."

John reached for his radio and then hesitated. "Are the Genii watching the radios?"

"The monitoring program's running. They'll see if you talk to each other."

"How many in the control room?"

"Two."

"Good."

* * *

The Stargate was activating as John reached the control room; he registered it from the corner of his eye, intent on taking down the man at the control panel. One punch laid him out and John pulled up the shield, encrypting it quickly. 

Three men had made it through, and a blonde he vaguely recognized as Sora appeared from somewhere. John ran, firing blindly behind to discourage pursuit.

He hesitated when the communicator came to life. "_Major Sheppard. I have a proposition for you,_" Kolya said.

"Ford and Teyla hear you," Alice murmured. "Teyla doesn't know Kolya."

"Kolya, I'm having a hard time keeping up…what's the score again?" John asked lightly.

"_My men have informed me that not only have you disabled some crucial generators…but you've stolen key components that make it impossible to be restored."_

"Yeah, I did that."

"_There are two flaws in your plan."_

"Always open to constructive criticism."

"_One. The assumption that I would believe you would rather destroy the city than let it fall to us…is childish."_

"Doesn't sound like me."

"_Second. If and when I determine Atlantis unsalvageable, Doctors Weir and McKay become obsolete."_

"Weir's alive?" John said in mock surprise.

"_Doctor McKay was able to make a strong case for keeping her alive…"_

"Let me talk to her," he demanded.

"_Sheppard!_" Elizabeth said a moment later. _"We're both here!"_

"It's good to hear your voice," John told her.

"_Yeah it's good to hear,"_ she agreed.

"_We have less than one hour until the storm hits full force. If the power is not returned to grounding station three within the next 10 minutes Dr Weir dies."_

"Again, you mean?" John snapped.

"_Her death will buy you another 10 minutes. After which should the power still be out, Dr McKay dies. We will then leave with what we can, and the city will be destroyed."_

"Well that's not enough time!"

"_If you don't mind destroying Atlantis, stay where you are for the next 20 minutes. Starting now."_

The communicator flipped off and John looked at Alice. "His own people are afraid of him," she warned him. "He may do it. He has nothing to lose."

"Thanks," he muttered. "What's happening at the reactor?"

"He pulled the guards away. Your path's clear, from here."

"Good. I'll see you there, then."

* * *

The reactor was almost fixed when Alice hissed, "The guards are coming." 

"Almost there," John muttered, slotting a crystal back into place.

"John..."

"Stop!" Two guards appeared, weapons aimed at him.

"Look, your boss wanted me to turn this thing back on…so I think we should do what he says."

"Be quiet." To his communicator, he added, "Sora? We have him."

"_Keep him alive. I'm on my way."_

"I don't mean to be a bad prisoner or anything, but Kolya is going to kill one of my people if I don't get this thing back on in time, so—"

"Turn around," the guard ordered.

John hesitated, grinning suddenly. "You turn around."

"What?"

"If I have to turn around, you should turn around."

A Wraith stunner spat and both guards fell, revealing Ford behind them.

"What the hell took you guys so long?" John demanded, turning back to the generator.

"Well, there's a storm…" Ford started.

"Just hold that thought." He slid the last component into place.

"That did it," Alice reported. "Power's back to the grounding station."

"You ok, sir?" Ford asked.

John nodded to both of them. "I've been better…I've been worse. My shoulder's a little sore."

"You want me to take a look at that?" Beckett offered.

"Take a rain check, doc."

"We should leave this area. More Genii will be on their way."

"I couldn't agree more," Beckett said quickly.

"John, one of the Genii is down the corridor," Alice murmured. "She's listening to us."

"Let's go," John told the others, sending Ford out first to watch.

"She's armed, but she's not holding it," Alice continued. "And she's going to keep following, I think."

"Watch her," he breathed, gesturing Beckett out after Ford and following, letting Teyla take their six. Louder, for everyone to hear, he continued, "McKay figures if he can harness the storms lightning he can fire up the shield."

"This lightning?" Beckett asked in surprise.

"SG teams have done it before to power the Stargate," Ford reminded him.

"There's a big difference between powering a star---"

"I didn't say you could talk."

"What kind of plan is that?" Beckett asked John, ignoring Ford.

"A Rodney McKay kind of plan. It's all we got."

"Which means there's only one place to go…" Ford murmured.

"Where the Genii will also be," Teyla agreed grimly.

"Anybody left in the hallway…is as good as dead," John told them.

"John," Alice murmured. "The Genii behind you has just defied orders to go to control. She wants Teyla."

"Will the young hunters in the Jumper be safe?" Teyla asked.

"Jumper bay is part of Stargate operations so they'll be protected," he said absently.

"So maybe that's where we should be headed," Ford suggested.

"Once the shield goes up over the city, Weir and McKay are expendable to Kolya. We've got to take the control room first."

"Would he really kill them because they are of no further use to them?" Teyla asked.

"No, he'd kill them to punish me. Now here's the deal. Ford and I get into position just below the control room stairs. Teyla and Beckett head for the Jumper bay."

"I intend to fight alongside you," Teyla protested.

"And I intend you to fight with us. Once you get in position lower the ship into the gateroom, open the weapons pods; that should create a distraction for Ford and me to go in. We take back the control room…get the shield up…city safe…Weir and McKay safe. Take the rest of the day off."

"And Teyla safe from the Genii. Smart," Alice muttered.

"Sounds like a plan, sir," Ford agreed.

"Stay on channel 2. Let's move out." To Ford, he added, "You're not gonna need that thing. Shoot to kill."

Ford left the Stunner behind, following him towards control. Teyla and Beckett headed in the other direction.

* * *

John paused at the base of the control room stairs, clicking his radio. "We're in position." 

"This isn't right," Ford said quietly.

"What?"

"Teyla and Beckett should of easily have made it back to the Jumper bay first. They should have been waiting for us."

"Teyla, what's your position? Teyla?" He looked around, catching Alice's eye as she came down from the control room.

"The Genii caught up to her," she answered his unspoken question. "They're fighting...she's winning, I think. Beckett's unconscious. And the Genii are about to evacuate, they're taking Elizabeth and McKay with them."

"Damn," John breathed as the Genii entered the 'Gate room. "Change of plan. You get McKay."

"Seriously, this is a bad idea!" McKay protested as he was forced downstairs. "You saw what happened to my last plan…this is not what yo---"

John fired, killing two soldiers. McKay jumped, dashing for safety; Koyla, out of John's range, grabbed Elizabeth, holding her tightly.

"You're not going anywhere," John warned him. "I will shoot you if you don't let her go."

"And risk hurting Dr. Weir?" Kolya backed towards the 'Gate, yanking Elizabeth with him.

"I'm not aiming at her." He shot, hitting Kolya dead on and knocking him into the gate. Elizabeth stumbled away, catching herself. "Find Teyla and Beckett," John told Ford. "Make sure that's all of them." He caught Elizabeth's arm as she rose, steadying her. "Sorry about that, I had to, ermm…you okay?"

"No," she said dazedly.

"You will be. Come on." He led her up to the control room where McKay was already working at the console.

"Wait! What are you doing?" Ford asked.

"I thought I'd activate the shield and save the day. You got something else in mind?"

"Teyla and Beckett are still out there," Ford reminded him.

"Tracking system's down. There's a tsunami headed towards the city. Two and a half minutes they're dead." McKay was still typing, determined to get the shield up.

"Then give them two minutes," John ordered.

"Teyla's still fighting the Genii girl," Alice told him. "Still...not losing."

John clicked his radio on. "Teyla and Beckett, fall back to the control room."

"There's no more time," McKay said firmly. "Either we lose them or we lose the city."

"They're coming," Alice said suddenly. "The Genii's helping them."

The two women appeared, supporting Beckett, and Elizabeth turned to McKay. "Rodney, go!"

"Going."

"What's happening?" she demanded, when nothing seemed to happen. John blinked when Alice flickered again, turning away from the group.

"It's working," McKay assured them, "it just needs to build up enough power for the shield generator to activate. Wait for it..." For no particular reason, he added, "Carson."

"Rodney," Beckett answered dazedly.

"Just in time to see how this ends huh? Now."

On the display they watched the shield power up just in time, as a wave that would have drowned the city broke over them. "Nice work, Rodney," Elizabeth said in relief.

"Did you ever doubt me?"

"Yes. Several times."

Deflated, he muttered, "Oh."

"I see you've made a new friend, Teyla," John said brightly. Teyla gave him the 'you idiot' look and he glanced away casually.

* * *

It took a while to sort out the city, but eventually the displaced personnel began to 'Gate back. John stood on the balcony with Elizabeth, watching them. 

"What do you want to do with her?" he asked, continuing a conversation about Sora.

"Oh, I don't know yet. We'll keep her locked up for the time being. Maybe releasing her to the Genii will help ease tension." Elizabeth was only half-listening to him, watching her people come home.

"You're extremely optimistic you know that?"

"You think so?"

Rodney wandered up, one arm wrapped in a bulky bandage. "Everyone getting back ok?"

"It looks like it," John told him.

"How fares our city?" Elizabeth asked him.

"Well…we've begun pumping out the lower levels of the east peer which was flooded. There is structural damage but nothing to serious. Beckett suffered from a minor concussion…as for me look at this." He gestured to his arm. "I had to do this myself. Still…on the bright side I've had my first decent meal in 24 hours so…all things considered I'd say we are just fine."

"You say these things happen every 20 years, right?" John said idly.

"That's what they tell us," Elizabeth agreed.

"How far in advance can we book days off?"

* * *

When the 'Gate finally shut off Rodney went to oversee the start of the repairs; Zelenka was going to take charge of them, but Rodney wanted to make sure they got started ok. Elizabeth wandered into her office; she wasn't working when John glanced in, but at least she was off her feet. He made a mental note to check on her later and went to walk the city. 

Alice didn't appear for a long time, not until he'd circled some of the deserted areas and was heading back towards the main area. "The generators are all back online," she reported. "And Zelenka thinks he'll be able to fix the control panel for the grounding station."

"Good," John agreed. "How about you?"

"Me? What would be wrong with me?"

"I saw you. When the generator went out, and when the lightning hit."

"Saw me what?" she asked, seeming genuinely curious.

"Flicker. You told me the generator wouldn't affect you."

"It didn't," she agreed.

"It did," he contradicted her.

Alice smiled faintly, looking away, and he insisted, "Tell me what happened."

"Some of the systems run off more than one generator, for backup. Mine is one of those. I run off three of the generators, all the time, and if all three go down I switch automatically to another. The first one you hit was one of mine, the second wasn't, and when the lightning hit it sent much more power than the city usually uses through all the circuits. That's all."

"You told me you weren't running off that generator."

She shrugged. "I wasn't running off only that generator. And it had to be done." Catching his look, she added, "I'm a servant of my city and of you, John. I do what's needed. That's how I was made."

"Even if what's needed would destroy you?" John ignored the other part of the sentence, not wanting to deal with it right now.

"If you hadn't stopped the Genii, the city would have burned or drowned. Running at a little less power than usual wasn't such a big deal in comparison. You won, John. That makes it all worthwhile."

"Yeah," he said slowly. "Thanks for your help."

"What I'm here for," she said, turning away and vanishing midstep.

"Yeah," he breathed, heading for his quarters.


	4. Hot Zone

Author's note: Hey titan5, glad you're still enjoying. Everyone else: where's my reviews:)

Hot Zone

John was really growing to hate practicing with Teyla. Especially since he generally spent more time flat on his back than he did actually fighting.

Case in point, as Teyla grew tired of dancing and, in three moves, had him disarmed and on his knees, choking on her staff.

"You have not been practising," she said disapprovingly.

"Yes I have," he protested.

"If this was really a fight ..."

"If this was really a fight, I would have _shot_ you by now." Teyla let go, shoving him forward. "Y'know, no matter how many hours I put into this, you're still gonna kick my ass."

"It is not for the winning that we practise," she reminded him.

"Well, what's the point?"

She rolled her eyes at him, picking up her bag, and he scrambled to his feet to follow her. As they headed for the door, the city PA came on and they paused to listen.

"May I have everyone's attention please?" Elizabeth said. "We have run into a questionable medical situation and at Doctor Beckett's suggestion we have decided to put the city into a self-regulated quarantine. For at least the next couple of hours, I need everyone to stay where they are, and report anyone moving freely through the halls. I hope you'll understand. Thank you."

"What the hell is this?" John said in surprise, swinging his bag off his shoulder and searching through it. "Did you bring your radio?"

She dug it out and passed it to him, watching him pace. His call to Elizabeth was intercepted by Bates; they spent a few moments arguing before she joined the conversation.

"McKay and Ford are both down there? I'm going after them."

_"We're in quarantine, John," _Elizabeth reminded him.

"Military head is supposed to be consulted in situations like this," John said tightly. "I'm ranking military officer here."

_"Yes, I'm aware of that, Major. You were off radio and we had to act quickly. Now, this is all protocol that was put into place long before this expedition began. Bates is here with me and we agreed this was the best plan of action."_

"Alright, alright. Teyla and I are coming up to join you."

"_We're in a _self-regulated quarantine_, Major. Everyone stays where they are_."

"We're nearly a mile away on the east pier," he protested. "D'you really think I'm in any sort of danger walking from here to the Control Room?"

_"At this point we don't know where they contracted the virus. This is a medical situation, John. Only authorised personnel in hazmat suits are allowed to roam freely – those rules apply to everyone, including you."_

"Well, then, get someone to bring me a hazmat suit," John said very slowly, fighting his temper.

From her tone, Elizabeth wasn't doing much better. _"Everyone in hazmat is busy configuring the lab to deal with a possible outbreak. Now __if_ _an opportunity arises, I will send somebody to come get you, but in the meantime, radio contact will have to do."_

Alice put her head around the door, looking faintly curious, and he caught her eye. "Alright," he told the radio. "Just ... keep us in the loop."

"_Will do_," Elizabeth agreed, and the radio went dead from her end.

John stalked over to the bench, as far from Teyla as he could get in the room, and dropped his bag onto the bench. Under the noise, he hissed "Where have you been?"

"Around, like always. Did you want me?"

"We need to work on your initiative," he muttered.

"I'm not programmed for initiative."

"Next time a deadly virus breaks out of a lab, _tell _me, all right?"

"All right," she agreed, sitting on the bench.

"John?" Teyla said carefully. He turned to find her closer than he'd thought, watching him. "Are you speaking with someone?"

"Thinking out loud," he said quickly.

She studied him for a moment before nodding. "I believe I shall practice. Please, don't allow me to disturb your--thinking."

"You go right ahead and practice," he agreed. "I'll just..."

"Think," she finished for him.

He waited until she was engrossed in the movements to murmur, "Tell me what's happening."

Alice sguirmed on the bench, tugging at her top to resettle it. "Two of McKay's team found a viral research lab. They were careless, and the virus has spread. Three have died so far."

"What kind of virus? What's the cure?"

She shook her head. "All workstations within that lab are isolated from the main system. I have no access to their database." She hesitated, glancing away. "One of his team is running."

John gestured for her to continue. "Peterson. They're trying to stop him fr...ow! John, he's rewiring the door controls. Badly."

_"Major Sheppard?" _Elizabeth said suddenly.

"Yeah, we're here." Teyla propped her sticks against the wall and came to join him--barely out of breath, he noted enviously.

_"We've lost another of Rodney's team."_

"Who?" Teyla asked quickly.

_"Dumais."_

John closed his eyes, taking a deep breath. "What does Beckett say?"

_"He doesn't know yet. They're doing autopsies now; hopefully they'll tell us something."_

"Everything else all right down there?"

John was carefully avoiding Teyla's gaze, but he could feel her staring at him. _Yeah, she definitely suspects something, _he thought tiredly.

_"Peterson's attempting to make his way back to the city," _Elizabeth said reluctantly.

"Someone has to do something."

"_We __are__ doing something_" she said irritably. "_Grodin's working on a plan to limit the door controls ...__"_

Alice was shaking her head. "That's not good enough," John interrupted Elizabeth. "Someone has to go out there and stop him. Teyla and I are ready."

"_Major, we've been ..."_

He interrupted again. "Peterson obviously isn't thinking straight and he's endangering the entire population of the city."

"_We don't yet know the nature of the virus we're dealing with. This is still a __medical__ situation."_

"Oh, we don't have time for this. I'm heading out." He rose to his feet, heading for the door.

"_Grodin, seal the gym," _Elizabeth ordered.

The door slid closed; John pulled up just short of walking into it. "What the hell is this?"

"_You said so yourself – you are the ranking military officer. I can't chance you getting infected._"

"I can't chance _you_ getting infected," John retorted. "Bates?"

"_Yes, sir_."

"Unlock the gym."

Teyla was watching warily; she started to protest, hesitating when Bates answered "_Yes, sir_."

"_Stand down, Bates,_" Elizabeth ordered. "_You are not in command here, Major."_

"Well, we'll agree to disagree. Bates, open the door."

"_Don't_."

"Elizabeth, he's heading right for you," John said frustratedly.

"He'll reach Control within ten minutes," Alice agreed.

"_So we'll stop him. We'll talk him down, we'll block his way, we'll ..."_

"Sergeant Bates," John said formally, "I am ordering you to open up the doors between the gym and the med lab right now."

A moment later the door slid open. Teyla turned away, hiding a look of disgust, as John said "We're heading out." She followed him as he headed off at a run.

* * *

In the lab John pulled on his suit so fast he almost ripped it. Teyla was slower, more precise.

"You should not have undermined Doctor Weir's authority in front of Sergeant Bates," she told him.

"Sometimes Elizabeth makes a decision early on and gets locked into it. That's a problem."

"She is not the only one who suffers from that affliction," Teyla said blandly.

John grimaced, touching his radio. "Doctor Weir, this is Sheppard. Teyla and I are ready to head out. What's Peterson's location?" She didn't answer, and he pressed, "_Elizabeth_."

"E19-3," Alice offered.

"He's in section E19, level three," Elizabeth said finally.

John pulled his helmet on. "Let's head out," he told Teyla, glancing at Alice before leading the way.

* * *

"Stop," Alice said a few minutes later, and John halted.

"What?" Teyla asked, pausing, but before he could answer their radios clicked on.

"_He's just beyond the door," _Grodin told them.

"Thanks, Grodin," John said, gesturing Teyla into position.

"Now," Alice said, stepping to one side as the door slid open.

"Doctor Peterson, I presume," John said lightly.

Peterson lifted his hands in surrender. "I'm not going back there."

"You don't have much of a choice." He started to ease back, towards the doors he'd just come through, and John's voice sharpened. "Easy."

"I go back there, I get infected. That's murder."

"Once we ensure that you are _not_ infected, you will be allowed back into the city," Teyla said soothingly. "Until then, you are a threat to the rest of the population."

"You won't shoot a member of your own team." Peterson dropped his hands, stepping forward.

"He's infected," Alice said warningly, and John raised his gun.

"Peterson. You will _not_ be allowed to go back to the city."

Peterson stopped, lifting his hands again. "OK, wait, wait, _wait_ a second. Take me back to the medlab, just quarantine me there. I'll go voluntarily – just please don't make me go back there." He glanced back at the open door with barely-concealed panic.

John glanced at Teyla and found her watching him, waiting for his decision.

"Really, I'm-I'm fine," Peterson told them. "I'm fine. I feel perfectly fine."

"He's infected," Alice said again. John nodded sharply, lifting one hand to his radio.

"Doctor Weir, this is Sheppard. Peterson has agreed to go back to the medlab until we can get this situation resolved."

"John!" Alice said abruptly. Peterson was dashing for the nearby transporter, almost there before John or Teyla had even noticed.

"Stop!" John lifted his gun, shooting at the doors. Peterson yelled, sagging as the door closed.

"Mess ha..." Alice vanished mid-sentence and every door in view slid closed. John halted in the act of reaching for the transporter controls, staring uneasily around.

Alice reappeared. "..ll. That was odd."

"What's happening?" John asked. On the radio, everyone was talking over each other, and his question didn't garner any attention.

"Medical lockdown. Atlantis knows Peterson's infected. He got to the mess hall and now the city's locking everyone down."

Grodin and Elizabeth had figured out the same thing; over the radio, she asked, _"Why now? Why not when Johnson and Wagner became infected?"_

"_The city's detection systems might have been affected by the flooding in those areas,_" Grodin guessed. "_Once Peterson entered the Mess Hall, the pathogen was almost instantly detected by automated systems and the city protected itself."_

"_Alright, what are my options?_" Elizabeth asked.

"_Limited. As of now, we're completely locked out of the mainframe."_

John took a few steps, pausing when a door slid open.

"Thought we were in a lockdown? Why'd that open up for us?" Clicking his radio, he said, "Weir, this is Sheppard. Were you able to get the transporters online or not?"

"_Doesn't look promising," _she said._ "Atlantis itself seems to have somehow sensed a threat and taken over most of the controls_."

"So it shut down the transporters?" John glanced at Alice, who nodded.

"_That's right_," Elizabeth agreed.

"Well, I wish _we_ would've thought of that," John muttered.

When Elizabeth answered he thought he might have finally pushed her too far. "_We __did__ think of that, Major. That entire section had to be powered up for you to open the door to Peterson. In fact, if you hadn't gone after him, he wouldn't have been able to __use__ the transporters._" She let that sink in for a moment before adding, "_D'you still feel it was a good idea?"_

"Where'd he transport to?" John asked, ignoring the surge of guilt.

"_The Mess Hall. Thankfully everyone _else_ respected the quarantine – there's only a handful of people there."_

"Alright, you've made your point."

"_Make your way back to the city. Wait in Beckett's lab for further instructions."_

* * *

Teyla didn't try to talk to John as they walked through the silent city. Alice didn't keep pace, either; every so often she appeared, gave him an update on McKay's team and then vanished again.

When they were almost at the control tower John sent Teyla on ahead; she didn't question it, ghosting out of sight. Alice watched curiously.

"What's up with the quarantine?" he asked.

"I'm sorry?"

"It's not stopping us."

"You're not infected." John stared at her, and she added, "That was the point of that outfit, wasn't it? You're not infected, Teyla's not infected, so the city lets you pass."

"That's something you're doing?"

She shook her head. "It's in the..." She said the word in Ancient, and then corrected herself. "Protocols. Infected people need to be taken care of."

Teyla reappeared at the end of the corridor. "I went all the way to the tower. I met with no obstacles."

John touched his radio. "Doctor Weir?"

"_Yes, Major?"_

"We've reached the city, but we haven't hit the city's quarantine. Are you sure it's locked you out?"

"_Pretty sure. I can't even get into my office."_

"Hasn't given us any trouble yet."

Behind Elizabeth, Grodin suddenly realized why they were safe. John swallowed a sigh of relief; he hadn't been looking forward to working it into the conversation.

"If that is the case, we should make our way to the Mess Hall," Teyla said. "I imagine everyone there will be very scared and confused."

"_I agree,_" Elizabeth said. "_Get to the Mess Hall and report back."_

* * *

"It's not a virus," Alice said abruptly.

John stopped, glancing around. "Teyla, why don't you..."

"Examine this empty corridor?" she suggested. "Perhaps I shall."

"Oh, she definitely knows about you," John said, watching her leave.

"She knows you know things you shouldn't. That's all."

"Not a virus?"

Alice shook her head. "Nanotech." Off his look, she added, "Cell-sized robots. Designed to help. Hurting, in this case."

"Gathered that much, thanks." He sighed, tugging at the suit. "This still necessary?"

"The city won't recognize you as uninfected if you're not wearing it. Certainly not if you go in there." She gestured to the mess hall.

"Figures." He tugged it again, glaring at her. "Can you pretend to be sympathetic? No, wait. You're not programmed to be sympathetic, right?"

Alice considered that for a moment before saying, "Teyla's coming back."

"What, you're programmed to avoid the question now?" he muttered as Teyla came up to him.

"Ready?" she asked.

"Yeah. Let's go."

Alice slid past, entering the mess hall ahead of him; turning, she told him, "I couldn't figure out which bit was the question," before turning again to step over someone. The group had been isolated for a long time with only Elizabeth's sporadic updates and Peterson's body for company; they mobbed John and Teyla on sight, demanding answers.

"We have yet to determine how one contracts the virus," Teylas said patiently. "It is _very_ possible that none of you have been infected."

One of the group—a lieutenant John couldn't see clearly enough to identify—demanded, "Then why are you in hazmat suits?"

"Just as a precaution."

John's radio buzzed, and he tapped it automatically. _"Major Sheppard, this is McKay."_

"What is it?"

"_I could use your help at my lab."_

John glanced at Teyla, who waved him away. "Go. I will be fine."

John nodded, turning quickly to go.

* * *

"Alright, McKay, I'm here."

"_D'you see it?"_

"Is it the big thing in the middle of the room?"

"_Yeah, that's the one."_

John studied it warily. Most of the machine was hidden beneath "Caution" and "Toxic" stickers.

"Should I pay attention to all these warnings?"

"_Not today, no."_

"It's harmless unless you have a pacemaker," Alice added.

"What's the plan, here?" John murmured, pushing the buttons McKay told him to.

"He's going to set off an EMP to knock out the nanobots. He's smart," she said admiringly. On the radio McKay was explaining the same thing to Ford, with rather more emphasis on how smart he was.

"Will that work?" John asked, studying the machine.

"The idea is sound. An EMP will kill the nanobots."

"And in practice?"

"_Major?_" McKay said abruptly.

"It's working. When should I hit the discharge button?"

"_OK – there should be a red overload light."_

"Yeah, I see it."

"_Wait til it comes on, give it a good ten count, and then discharge."_

"A ten count?" John repeated.

"_Don't worry – I've probably been around more EMPs than anyone."_

"This is gonna be, uh – I'm gonna be fine, right?"

"Do you have a pacemaker?" Alice enquired, apparently serious. John made a face at her.

"_Yes. That's a yes – you'll be fine."_

The light flicked on: John counted to ten before hitting the discharge button. The generator slowed to a halt.

"_Anything?_" McKay prompted him.

"_Is it possible it might take some time?" _Elizabeth asked hopefully.

"_Doubtful,_" McKay said with a sigh. _"Are you still locked out of the Ancient mainframe?"_

There was a pause before Elizabeth asked, _"Got any other ideas?"_

"John," Alice murmured.

He flicked off the mic on his radio, sighing. "What is it?"

"In the mess hall...it's started. You have no more time."

"_Major?"_ McKay said suddenly.

John flipped the mic back on. "Yes, Rodney."

"_We need to fix the generator. Listen..."_

Five minutes later, John stopped trying to follow McKay's increasingly panicked suggestions. "I've already tried that – it's blown."

"_That is before we re-set the sub-switch."_

"Well, maybe we shouldn't have overloaded it so much."

"_Look, it's fixable, it's fixable – we just need to use a little trial and error."_

"Look, even if we get this thing working, who's to say the pulse is gonna get any bigger? Ford and Zelenka have twenty minutes before their arteries rupture. Are you _sure_ an EMP will kill this thing?"

"_Yes."_

"Alright. I have an idea."

* * *

"This is a bad plan," Alice warned him.

"Help, or get out of the way," he ordered. Alice stepped to one side and he began disconnecting one of the generators.

To his radio, he added, "What do you mean, no?"

"_It's too dangerous,"_ Elizabeth said.

"You'd rather lose a third of our population?"

"_We're not there yet, Major."_

"We _are_ there! Ford and Zelenka are next. The people in the Mess Hall have a little over three hours. This is a full-blown outbreak. People are gonna keep dying unless we do this."

"_Even if we were able to get the EMP generator back online, the chances are slim that we would ever be able to get it powerful enough,"_ McKay added.

"_Can we bring the infected to the generator?_" Elizabeth suggested.

Behind her, Grodin quietly vetoed that, and McKay insisted, "_The major is right – the only way to create an EMP strong enough to wipe these little guys out is to ..."_

"_... to detonate a nuclear explosion in the atmosphere! Yes, I heard the first time!" _she protested.

"_I know it sounds severe,"_ McKay admitted, "_but if the major was able to overload a naqahdah generator twenty miles above the city, it would be perfectly safe from a radiological standpoint and the ensuing blast would be capable of creating a devastating electromagnetic shockwave – definitely enough to knock this virus out."_

"It's worth the risk," John said.

After a moment, Elizabeth said, _"OK. You have a go."_

He quickly finished packing the generator up and turned away.

"Your 'Jumper's ready," Alice said quietly.

"Thanks," he told her, hurrying past.

* * *

"You're almost there," Alice said. John nodded, eyes on his display.

"I'm almost in position."

"_Understood,"_ Elizabeth said. _"Would the EM pulse have any effect on the Puddlejumper?"_

"I'm hoping not. Either way, I'm more worried about the shockwave."

"_Good luck."_

"You too."

"_You're only gonna have thirty seconds once you release it before it explodes," _McKay said again. He'd given the same advice at least three times now. _"You need to get as far away as you can."_

"Get as far away from the nuclear explosion as possible – that's good advice, Rodney, thanks!"

"_You're welcome."_

"I'm releasing the generator ... now!"

The 'Jumper dived steeply; Alice vanished, and John concentrated. In the background, Grodin counted down the seconds to zero.

The 'Jumper rocked crazily; John fought the controls, flinching when he caught sight of the explosion. Finally, he got the ship under control and aimed for Atlantis.

"_Major, do you read me?"_ Elizabeth asked.

"This is Sheppard. I've cleared the blast – I'm returning home."

"_I'm glad to hear it, Major."_

"Did it work?"

"_We're about to find out."_

"_You should know almost right away," _Rodney said uncertainly. _"The pulse only lasts a couple of microseconds and then ..."_

"_The city's already ahead of us, Rodney,"_ Elizabeth said. _"You have a green light to return."_

John smiled as Atlantis came into view. "I'm almost there. See you in a few."

* * *

He wasn't exactly avoiding Elizabeth. Or Teyla. Not really.

Sighing, he decided to get one of them over with at least, and made his way to Elizabeth's office. Grodin smiled vaguely as he passed through the control room; John didn't stop, tapping on her door frame and sitting down.

"Are you OK?" she asked, studying him.

"Yeah, just a little nuke – nothin', really."

"The naqahdah generator plan was very clever. Good work."

"Thank you. Now, I'm going to bed." He stood up, thinking for one second that he was going to get away with it.

"We need to discuss what happened earlier," Elizabeth said, not looking up.

"Now?"

"That can never happen again."

John nodded, coming back to sit. "Look, I'm sorry about ..."

"I understand your expertise in military matters," she interrupted him, "and I agree that I should defer to those expertise in such situations."

"Thank you!"

"_But_ you are not the one who decides what is and what is not a military situation. Now, both General O'Neill and Colonel Sumner warned me that you don't respect the proper chain of command."

John shifted uncomfortably. "Well, sometimes I see a situation a little different than ..."

"No. Listen to me, John. Now, you endangered yourself and the lives of many others."

"Because I thought it was the best course of action to take – and, by the way, I saved your ass."

"I know you did – but you have to trust me."

"I do!" he protested.

She studied him for a minute. "Do you?"

He was saved from answering when Rodney and Carson came in, talking over each other about the virus. John escaped as soon as he could, leaving them still discussing conspiracy theories.

He didn't realize where he was going until he found himself outside Teyla's door. Sighing, he murmured, "Alice?"

She stepped out of a door further down the corridor, and he blinked. "Why do you do that?"

"Why do I do what?"

"You vanish into thin air, but you always come from somewhere. Why?"

"I'm supposed to. The People thought it was less surprising. Disappearing is fine; _ap_pearing is not." She shrugged. "I'm not..."

"Programmed for psychology, I know. Is Teyla asleep?"

"Not anymore."

John grimaced, touching the door sensor. "Go away."

She smiled faintly, deliberately walking away.

Teyla's door opened, and she studied him. "You are uninjured."

"I am," he agreed.

"Do you wish to come in?"

John peered uncertainly around her door. "Halling isn't hiding in there to defend your honor, is he?"

"I believe I can defend my own honor, John. Did you wish to speak about Atlantis?"

"I..."

"John," she cut him off. "Atlantis answers to you as to no one else. We all know this. It is not something to be ashamed of."

"I'm not ashamed, exactly, it's just..." he shook his head, unable to explain it. "It's...I can't explain it. Even Carson doesn't feel it."

"She warns you of danger," Teyla said slowly.

"When it occurs to her, yeah. She's..."

"John," she said again, cutting him off. "Atlantis speaks to you. This is something to be glad of. Certainly, if she is trying to help you. If you wish this kept a secret, I will."

"It's not a secret," he said carefully. "But I don't want to volunteer it, either."

"Agreed," Teyla promised. Turning her head slightly, she added, "Atlantis? In future, please tell John I am sleeping whether it is true or not."

"Oh, yeah. Teach her to lie. Brilliant." John smiled faintly. "Thanks, Teyla."

Teyla reached for his shoulders, leaning her forehead against his. Letting go, she pushed him back lightly. "Get some sleep, John."

"See you in the morning, Teyla."

"Good night." She took a step back, and just before her door hissed closed John heard her add, "Good night, Atlantis."

"Want me to tell her to call you Alice?" he asked as he headed for the transporter.

"Alice isn't my name," she pointed out. "And you can't tell her now, she's asleep."

"Traitor," John said mildly. "'Night, Alice."

"Sleep well, John."


	5. Sanctuary

Author's note: Wow, appealing for reviews really worked! Cool.

lakewater: Here you go.

Titan5: Yeah, I'm getting very fond of Alice. And I liked that line from Teyla; sort of accepting the hold the city has on him.

trecebo: I'm planning on going through the whole SGA series. Not every episode, cos there's no point if they're off-world, but most of them.

Duchcess67: That sounds interesting! Will you let me know?

TheNaggingCube: Yeah, I did love that line.

KansReader: Soon enough?

More reviews please!

Sanctuary

John was really starting to hate Wraith Darts. The tiny ships were faster than the 'Jumpers, even if their weapons weren't as strong, and usually they could swarm the Lantian ships.

"I count two...how about you?"

Rather pointedly, his HUD flashed a couple of times. He couldn't spare the time to glare at Alice, but he did think the display off.

"Yes, sir," Ford agreed. "I recommend shooting back anytime now."

"I'm trying. The hit must have caused some damage. McKay?"

"I'm on it." McKay scrambled out of his seat into the rear compartment, digging into the circuits.

"Where did they come from?" Teyla asked, studying the display intently.

"She's right. The Darts are short range fighters. There's probably a hive ship around here somewhere," McKay called from the back.

"Then we need to get out of here," Teyla said sharply.

"Yes we do," John agreed.

"There are no Hives within range," Alice offered. John ignored her, yanking the 'Jumper into a turn that pressed them into their seats and threw Rodney against the bulkhead.

"The Stargate is the other way, sir," Ford reminded him. "On the other side of the planet."

"Yeah, now we're taking the scenic route. McKay?"

"I'm almost there," he promised, poking at the circuits.

"That's not right," Alice murmured, but John didn't have time to react before Ford warned, "There's one on our tail!"

"Thank you. I know all about that one. Keep your eye on the _other _one."

"Okay." McKay pushed away from the circuits. "You should have weapons now."

"Negative," John said, yanking the 'Jumper around again.

"You sure?" McKay said in surprise.

"Positive."

"I'm pretty sure I fixed it."

"Well obviously you didn't!"

"Perhaps we could lose them in the atmosphere of the planet," Teyla suggested calmly.

"Two more Darts on our two o'clock," Ford warned.

"I see them. _McKay_?"

"It's not like I'm holding back on you!" McKay snapped, frantically switching circuits.

"That's not going to work," Alice said, addressing McKay even though she knew he couldn't hear her.

"Helpful, thank you!" John snapped.

"I'm doing my best," McKay protested.

The HUD snapped on again as a blast of something like static electricity shot up from the planet, washing through the 'Jumper and snaring the Darts. The Wraith ships vanished in the glare and when it cleared, they were destroyed.

"The Wraith darts have been destroyed," Teyla reported.

"Ah, that's a good thing," John pointed out.

McKay came into the compartment, sitting down. "I thought for sure we were dead. Anyone think we were dead?"

"He hasn't fixed the weapons," Alice protested. John waved her off, listening to McKay decide they'd been rescued by an energy weapon.

"Well, what do you say we find out?" he suggested, putting the 'Jumper into a low orbit so McKay could run his scans.

"So just to confirm we're all still definitely not dead," McKay said after a moment.

"I feel very much alive," Teyla said.

"Good. Same here." McKay fiddled with his computer.

"Wish I knew what that was," John said idly.

"Looked like lightning," Ford offered.

"Space lightning?" John said disbelievingly.

"I already said it's some sort of energy weapon," McKay said impatiently. "One that apparently destroys Wraith darts."

"Nice," Ford said uncertainly, "but...why them and not us?"

"Well assuming that we're still alive...and there doesn't seem to be any damage as a result of the pulse, I think we can safely conclude that ah...um...um...I got nothing." McKay shrugged. "I got nothing to conclude. I'm just...talking for the sake of talking."

"You're sure you're ok?" John asked, eying him.

"You know how much I hate certain death?"

"You're alive."

"It wasn't aimed at you," Alice said quietly. John glanced at her, unable to question her directly with everyone there; when he looked back Teyla was watching him curiously.

"Could something like that be...naturally occurring?" she asked.

"My money's on not naturally occurring," John said absently, catching Alice's nod from the corner of his eye.

"Like a weapon the Ancients left behind?" Ford suggested.

"Yeah. And any weapon that powerful would have to be powered by..."

"A zero point module," McKay realized.

"That's right," John said.

"Right well we need to get down there," McKay said, reaching for his computer again.

"I've got to put down, check for damages anyway...before we head back to Atlantis." John turned the 'Jumper towards the planet, easing out of the low orbit.

* * *

John lagged as the others left the 'Jumper, fiddling with his vest and equipment. "Alice?" he murmured once the others were off the ramp.

"This planet does not appear in my database," she said from the cockpit. John turned towards her.

"What about the weapon?"

"It's not a weapon. There are no traces of radiation, no residue of any kind."

"If it's not a weapon, what is it?"

She shook her head. "No information in my database. But it is not a weapon."

"No ZPM?"

"Not powering a weapon, no."

"John?" Teyla leaned in. "Dr McKay is eager to leave."

"Yeah, I'll bet," he agreed.

"Have you learned anything?"

John blinked, glancing back at Alice. "Nothing useful. No database entries for this planet." He followed Teyla out, snagging Ford's binoculars as they passed him.

"If there's a weapon down here, sir, these folks didn't build it."

"Not these kids," John agreed, studying the village just visible in the distance. To McKay, he added, "Picking up anything?"

"I'm picking up everything. Just nothing worth mentioning." He turned off the scanner, shoving it into a pocket.

"These folks look familiar to you, Teyla?" John asked, tossing the binoculars back to Ford.

"The Stargate is in orbit, Major," she reminded him. "My people could never have ventured here."

"Right. What say we venture?"

* * *

"Elizabeth's going to kill you," McKay murmured as they reached the 'Jumper.

"Why, just because we're bringing the religious head of a planet that may or may not be harboring a super weapon back to Atlantis without checking in first?" John shrugged. "She'll get over it."

"I just want to make sure I'm there when you explain that to her." Rodney grinned, heading into the 'Jumper.

John grimaced, glancing back. Chaya and Teyla were coming towards him, Ford trailing behind them.

"Alice?" he murmured, low enough that Rodney wouldn't hear him.

"Yes." Turning, he saw her standing on the ramp.

"We're bringing a guest to Atlantis."

"All right," she said.

"Keep your scanners on her, ok?"

"I will," she agreed.

"Good. Scoot."

Alice ducked back into the 'Jumper as Chaya and the others came into hearing range. "Ready?" Teyla called.

"Yeah." To Chaya, he added, "It won't take long to get to Atlantis."

"Thank you," she said with a smile, accepting his hand up the ramp.

* * *

"Welcome to Atlantis." Elizabeth did polite interest like no one John had ever met, and this time was no exception.

"Thank you," Chaya said politely, looking around the 'Gate room.

"I hope you don't mind, but our doctors do require a medical exam of all offworld team members and our visitors. But after that perhaps you would like a full tour."

"I would love that," she agreed.

"Major Sheppard has already promised to do so," Teyla said mildly.

"Of course he has," Elizabeth agreed.

"Of course I have." John raised an eyebrow, all but daring her to call him on it.

She ignored the challenge, turning to Chaya. "Please, if you'll follow me to the infirmary..." Chaya followed obediantly, smiling when John fell into step behind her.

"Maybe I should tag along in case you have any questions the Major can't answer," McKay suggested.

"I think I can handle it, Rodney," John said dismissively.

"There are a lot of systems you know absolute-"

"Got it covered," he insisted, chasing Elizabeth and Chaya. He caught a glimpse of Alice, watching from the balcony, but she didn't try to talk to him and he hurried after the women.

* * *

"How many of you are there?" Chaya asked later.

"Counting all the Athosians on the mainland? Might get a couple of hundred, which leaves a very large empty city. Right now we're living in one section because we don't have the power to spread out more than that. What do you think so far?"

She glanced away uneasily. "I think it's wondrous. But ultimately the decision is up to Othara. You're not a believer, are you?"

John stopped, catching at her arm to keep her with him. "Look, Chaya, I respect that you believe. Look...I can't talk to Othara. I can only talk to you so let me ask you this...What if the shoe was on the other foot? What if your people were in trouble and we could help you? Would you just take no for an answer?"

"It must have been very hard to live your entire life under the shadow of the Wraith," she said thoughtfully.

"Don't misunderstand me. Teyla and her people have known the Wraith forever, but when I say we're new I mean we _just _got here. From another galaxy...a planet called Earth."

"Earth?" she repeated, frowning.

"Very far away. You know those clusters of stars you see in the night sky? Some of them are called galaxies and they're even farther away from you than the stars. Earth is in one of those galaxies."

"You came through the Stargate?"

"That's right," John agreed.

"And can you not simply return?"

"Well, not simply. We knew going into it that it was probably going to be a one way trip--but we thought what we would find here would be worth the risk."

"And is it?" she asked.

John grinned lazily. "So far. Ask me again when the Wraith show up."

* * *

Out on the balcony she smiled, spreading her arms. "Oh, the ocean air is so invigorating."

"Plenty of that here, most of the planet's ocean." John followed her gaze, staring at the water.

"Surely there is enough land to resettle the refugees?"

He nodded absently. "Oh, there is...just can't guarantee their safety."

"Even though you control all of this?" Chaya gestured to the city around them.

"I'd be lying if I said we controlled it all." John looked away, towards the control tower. "This place is so far beyond us in so many ways. For example Atlantis does have a shield that can withstand anything the Wraith can throw at us but we have no way of powering it up...we can't risk taking in any more refugees than we have." Shaking his head, he turned back towards her and held out a hand. "Come with me."

She let him guide her back into the city, wandering through the corridors. "Major Sheppard...

"I'd prefer if you called me John."

"John," she said uncertainly. "How did you make enemies of the Wraith?"

John flinched. "That was my fault."

"Yours?" she repeated in surprise.

"I basically woke them up trying to rescue some people they captured, they didn't take too kindly to that."

"But you saved your people?"

"Most of them."

She nodded. "That is how you know for sure they are coming back."

"Yeah, we just don't know when." They reached the control room, and he started pointing controls out. "Main control console. Environmental support systems. Communications. This..." He hesitated, watching Grodin fiddle with a new console. "This is...uh...what is this?"

Chaya leaned on the console as Grodin answered without looking at them.

"Sorry, Major, we don't have the faintest idea what--what..." He trailed off as the machine lit up, looking up at them. "This is a new piece of equipment we found in another section of the city. It hadn't yet been initialized."

"You think she has..."

"She has the gene." Grodin grinned, running his hand over the console.

Chaya backed up, putting her hands behind her back. "Did I do this? What does the machine do?"

"We don't know," Grodin said absently. "Not yet anyway."

"Atlanteans are good at lots of things, but writing instruction manuals wasn't one of them." John stepped forward, gesturing towards Elizabeth's office. "We should probably wrap this tour up. I know Doctor Weir is anxious to talk to you."

"Will I see you after that?" Chaya asked, following him.

"And during." John grinned.

Elizabeth and Teyla were already in the briefing room, and McKay arrived on John's heels. After a few minutes of small talk Elizabeth got them settled at the table to begin the meeting.

"What we're proposing is a kind of land lease in which refugees rendered homeless by the Wraith could resettle on Proculus. In return we can offer you services and knowledge of benefit to your people."

"Such as?"

Idly, John thought that Chaya did the best dumb blonde impression he'd seen in a long time.

"Well, you've seen what technology we possess here...we can help you down a path to a more industrialized society, but at a pace that will maintain your planet's ecological balance."

"Your scientific knowledge is impressive, Doctor Weir, but we have no need of it. Othara provides us with everything we require."

"Well food just doesn't show up on the dinner table," John pointed out.

"You do plant all your own crops?" Teyla asked.

"Of course we do," Chaya agreed.

"We can show you ways to increase your crop yield," Elizabeth offered.

"We grow all the food we need to live," Chaya said serenely. "Anything else would be gluttony."

"Building materials then?"

"We have abundant timber and iron ore to forge what little metal we need. Othara is kind."

"There must be something," Elizabeth said. John blinked at the frustration in her tone, but Chaya didn't seem to have noticed.

"What my people value most is spiritual knowledge. What can your culture provide in that regard?"

Elizabeth frowned, leaning back in her seat. "Earth's people don't share a single spiritual belief. We embrace a number of different religions and philosophies: Christianity, Buddhism, Judaism, Islam..."

"Hinduism," John added. "Kwanzaa..."

"Interesting," Chaya said slowly. "Tell me about them."

"All of them?" Elizabeth said in surprise.

"Yes, they sound fascinating."

"Well—I am hardly competent to discuss all of Earth's religions...but I can offer you some resources. With very little training you could have complete access to our historical database."

"That would be wonderful," Chaya said brightly.

* * *

"Doctor Weir wanted me to make sure that Chaya saw everything," John said innocently.

"Everything," Teyla repeated skeptically.

John fought the urge to hide the picnic basket in his hands. "Well...not everything. Uh...Chaya mentioned she wanted to see the best view of the city at night which I think is at the top of the south west pier and...and since it's such a long walk I thought I'd bring along a few provisions."

"Continuing our efforts to secure a treaty." Teyla's tone was absolutely serious.

"Exactly. Yeah."

"As our...ambassador."

"I'm an ambassador and she is a... diplomat."

"On a late night..." she considered carefully before finishing, "picnic?"

"Yes."

Teyla smiled. "I know that as ranking military officer here in Atlantis that you feel a heavy burden of responsibility. But you are allowed to have feelings for others..."

"Ah no," John cut her off, "This is a...this is an ambassadorial diplomatic picnic outing thing."

"...Without having to justify that to anyone," Teyla finished. "Although I'm unsure what Atlantis will think."

"Your guess is as good as mine, she's not talking to me."

"Perhaps she is jealous," Teyla suggested, smiling. "Goodnight Major."

"Goodnight...Teyla." John watched her walk away, vaguely disturbed.

* * *

"Mmmm, this is delicious."

Whatever crops they grew on Proculus, they apparently didn't include strawberries. John grinned, watching her eat. "Well, enjoy it while you can because it's the last of what we have."

"Then I am honored."

"When McKay finds out he's gonna kill me," he said conversationally.

"Othara will save you," Chaya promised.

"Oh good."

She laughed, reaching for another strawberry. "Such wondrous things. I can't imagine you'd want to do anything but eat all the time with such a variety of foods."

"Well, we manage to pull ourselves away somehow."

"I've been learning much about Earth. Doctor Weir has got me on your—information machines."

John sat up, reaching for his glass. "Elizabeth's got you on a computer already, huh?"

"I am fascinated by your many religions. So many beliefs, so many philosophies."

"Yeah, we got a few of those."

"So many contradicting faiths." Chaya's voice was softer, sadder.

"That's a bit of a mess," John agreed. "More?"

"Yes please." She held out her glass for him to fill.

"We, uh...traded for grapes. The Athosians...Teyla's people—they make this on the mainland."

"I wasn't really truthful with you about something," she said abruptly, playing with her glass. "On Proculus when I told you I did not feel lonely--coming here and being with you reminded me what it was like not to be alone."

John flinched, rising to his feet and crossing the edge of the balcony for a moment before looking back at her. "What?" she asked gently.

"Well, I mean ... nothing. It's just that ... this is the first time I've been in a romantic situation with a woman from another planet, and it just strikes me as really, um ..."

"Wrong?" she asked sheepishly.

"No! God, no! Just, just funny. I'm sorry - I-I just thought that I would, uh ..."

"You said it yourself," Chaya pointed out. "We're both human."

"Yes, we are. And I'm really glad you didn't say 'family', otherwise I'd have to leave."

"You don't."

John took the hint and sat back down beside her. "I'm not going anywhere." Gently cupping her face in his hands, he kissed her.

* * *

Walking away from her quarters later, he was vaguely surprised to see Rodney waiting for him.

"Major."

"Rodney. What are you doing up so late?" Absently he glanced around for Alice; she was usually somewhere nearby when he walked the city.

"I was just, um, I couldn't sleep, so I was going back up to the Control Room to do a little research. What about you?"

"Oh, no thanks."

"No. I mean, what were you doing up so late?"

John frowned. "I'm always up late, Rodney."

"Word of caution? The whole Captain Kirk routine is problematic to say the least, let alone morally dubious."

John slowed to a halt. "What routine?"

"The romancing of the alien priestess? It's very 1967 of you. Actually, I'm surprised ..."

"If and when anything I do becomes your business ..."

"It becomes my business, _Major_, when an alien woman who is clearly not who she claims to be has the ranking military officer wrapped around her little finger!"

"Don't go there, McKay."

McKay shook his head quickly, desperately. "I'm sorry - I know I'm not normally Mr Sensitive, but you gotta believe me when I say there is something about her. I know it's intangible but I can feel it."

"I said don't go there!"

"It's just a matter of time before I prove it, Major. I'm just recommending that in the meantime you keep your .." He trailed off when he noticed Chaya's open door; she was listening, arms folded tightly across her stomach. McKay hesitated, starting to apologize; Chaya turned away, going back to her room, and John followed her.

He paused just before entering the room, murmuring, "Alice?"

For the first time since she'd introduced herself, the program didn't appear. Sighing, he slipped into Chaya's room.

* * *

"John?" Chaya said softly, late the next morning.

He glanced up from staring at the table. "Hmm?"

"You're distracted."

"Yeah. Sorry."

"What are you thinking?"

"I'm just wondering where...it's nothing." He changed his mind halfway through the sentence, looking up as the door open; Elizabeth and Teyla. McKay trailed behind with his laptop.

"I admit to being impressed by most of what I've read of Earth religions: the Torah, the Koran, the Talmud, the Bible. Most of them reveal a diverse and deep desire to grasp the divine." Chaya was watching McKay, though she was speaking to Elizabeth.

"So we do have something we can offer you."

"But I've also been reading about your history. Even now, somewhere on your planet, you are at war."

"Yeah, that's true," John agreed.

"I made no attempt to hide that fact from you," Elizabeth pointed out. "Chaya, we are definitely not perfect."

"There's a lot about you as a people that I find disturbing."

"Can that not be said of any people?" Teyla asked.

Chaya shook her head. "No. Every soul on Proculus is free from the hatred and the anger people from Earth seem to feel for each other."

"Come on, we're not all that bad. You know that," John protested.

"I do," Chaya agreed, laying her hand on his. Her gaze slid past him, and when he followed it he saw Alice standing, arms folded, against the back wall.

"They're scanning you," she said, and he frowned. When he looked back Chaya was listening attentively to Elizabeth.

"We're not talking about the people on Earth. I'm talking about every member of my expedition team here in Atlantis; and I'm talking about the friends we've met since coming here, like Teyla's people."

"There are some among you - yourself included, Doctor Weir - that I know Othara will welcome with open arms. But there are others ..." she trailed off, glaring at Rodney.

"I handpicked every member of this expedition, and I know Teyla feels as confident about her own people."

"I'm sure," she agreed coolly.

"At the end of the day, this is a matter of trust," Elizabeth said.

"Yes, it is, Doctor Weir. Have your scans found anything yet, Doctor McKay?"

McKay looked up, startled. "Um ... uh ... actually, no."

"What the hell is this?" John asked angrily.

"I'm sorry, Major," Elizabeth said. "There was cause for legitimate concern as to ..."

"... whether I was or not who I claimed to be," Chaya finished.

"I'm sorry, Chaya. I honestly felt it would do no harm."

McKay rose to his feet. "Stop apologising, Elizabeth. How did she know?"

"McKay!" John said warningly.

"She's an _Ancient_, Major."

"She's what?!"

Talking faster, McKay pressed on, "I'm right, aren't I? The perfect health, the energy weapon, the fact that she has the gene. It's the only logical explanation."

"What the hell are you talking about?"

McKay ignored him, focused on Chaya. "I just don't understand the act. I mean, you must know we'd give just about anything to talk to you, to learn from you. I mean, what is it? What, are you checking us out?"

Chaya sighed, pushing her chair back from the table. "I see that in my desire to come to Atlantis, I have revealed too much of myself."

"He's right?" Elizabeth said in surprise.

"I'm right?!" McKay repeated, equally surprised.

"I am what you call an Ancient. And it is also true that I can never offer your people sanctuary. But you are wrong as to why I came here."

"Why did you come here?" John rose, taking a couple of steps away.

"You, John."

"Me?" he repeated.

"I have lived in solitude for so long that when you asked me to come to Atlantis, I ..."

"Oh my God, he _is_ Kirk!" McKay sank back into his seat.

"This was never about, uh ..." John shifted uncomfortably, looking at the others. "Could we just have a moment to ourselves here?"

They refused loudly, and Chaya smiled. "That's alright. I've stayed here long enough." She rose to her feet, leaving the room. John chased her; he registering Alice keeping pace, watching them.

"C'mon, Chaya. You and your people are the reason we came here in the first place."

"I can't." She stumbled, reaching for him to catch herself. "I can't..." She collapsed into his arms, breathing far too fast.

"Her people are calling," Alice said quietly. Chaya stirred, pulling herself out of John's arms.

"No." She took a couple of steps, looking mildly dazed.

"What the hell was that?" John protested.

"They're coming for them. I should have never left them."

"What's going on?" John protested.

Chaya looked at him, seeing to really see him for the first time since she'd collapsed. "I'm sorry, John."

"John, get away from her," Alice said urgently. John stumbled backwards as Chaya's body dissolved, reforming into a glowing entity. The 'Gate powered up behind her, forming a connection without dialing, and the glowing being sailed into it.

"What just happened?" Elizabeth demanded from the balcony.

"There's only one way to find out," John said.

"Go," she agreed.

* * *

John ran through the pre-flight as he was sitting down; by the time he got the 'Jumper to the 'Gate room the wormhole was ready.

"_Major, are you sure you know what you're flying into?"_ Elizabeth asked.

"Pretty good idea. The Wraith are attacking Chaya's people."

"_You can't hope to defend them with one ship!"_

"I don't think I'll have to." He urged the 'Jumper forward, into the 'Gate.

Alice was standing beside him when they reached Proculus; the HUD immediately started flashing proximity warnings, most of which John ignored.

"Where have you been?" he demanded, firing two drones and rolling to avoid a Dart.

"In the city, like always. On your left."

"I see him." He fired again. "You didn't come when I called you."

"I was told not to—on your _left,_ John."

"I still see him!"

"I'm sorry, I must have been confused by the way you're not firing at him!"

John yanked the 'Jumper around, hard. "You are spending way too much time in McKay's computer. I've a good mind to ground you to the control systems." He finally managed to hit the persistent Dart, grinning in triumph. "You were told not to answer me? Who told you that?"

Alice didn't answer, and he glanced over. "Alice."

"I'm just supposed to help you fight," she muttered. "Ten o'clock."

"Who's giving you orders, Alice?"

"Ten o'clock," she repeated.

Light flared suddenly bright in the cockpit and when it faded, Chaya was standing behind them. "What are you doing here?" she demanded.

"I'm here to help you."

"Help me?" she repeated.

"To defend your people."

She shook her head. "Leave. I will take care of this."

"Please?" Alice said quickly. Chaya glanced absently at her.

"Yes, your restrictions are lifted." To John, she added, "Go home." She shifted into her light form, vanishing before he could react. The wave of light rippled out from the planet, destroying the Darts on impact; the 'Jumper didn't so much as rock.

The path back to the Stargate lit up on the HUD; John shook his head, starting towards the planet. "We're not going home yet."

"We were told," Alice protested.

"Chaya might be your boss, but she's not mine. Find her."

The HUD flashed his flight path, showing a course to land by the temple, and he pulled the 'Jumper around to follow it. "What'd she tell you to do, anyway? And when'd she get you? Not in the 'Jumper."

"Not in the 'Jumper," she agreed. "In the infirmary."

"Beckett was with her in the infirmary."

"She told him she was praying. She told me not to go to you, not to watch when you were together, not to speak to anyone or in any way imply that she was other than human."

"And you just agreed?"

Alice frowned. "Chaya is of the People. My program demands loyalty to her above you."

"Did it even occur to you to argue with her?"

They'd reached the surface, and she waited while he set down and powered off the major systems. "I asked her to reconsider," she offered.

"You did, huh." He leaned back to study her. "How'd she take that?"

"She refused to remove the restrictions. But she commended me for loyalty to you." She shrugged. "I was..."

"Wait, don't say it. You were following your program, right?"

For the first time in months, Alice sounded like the child she pretended to be. "I'm made to be useful. Without you I can't fulfill my function. I want to be useful."

"You are useful."

"To you."

"To the city. Chaya knew that, or she wouldn't have bothered shutting you up, right?" Alice smiled hesitantly, and he nodded. "Attagirl. Now, I've got to go find Chaya. Wait for me, all right?"

"Yes, John. I will."

* * *

Chaya was waiting in the garden for him; she looked miserable, and he fought down the urge to comfort her. "Is it Chaya, or Othara? I'm just curious."

"When I was a mortal, I lived here." She gestured around them. "This was my home. When those of us who you call the Ancients ascended, we were supposed to leave behind us all human ties. Some of us found that--difficult."

"So you couldn't stand by and watch your people getting wiped out by the Wraith."

"When their terrible fleet approached, I lashed out with my mind and with a single thought destroyed them all. The others of my kind did not approve of such interference in corporeal matters. And so I was exiled. My punishment was the unending protection of this world." She turned away from him.

"Why pretend to be human at all?" he asked, taking a step towards her.

"So that time to time I may walk among the people - know them as the good and kind souls they are. For thousands of years, I have come and gone to the villages, never staying too long to get attached to anyone ... until I met you." She stepped closer, watching him. "I have never regretted the choice I made all of these years - until now. I am permitted to safeguard my people, but my people only. This is my punishment. This is what _makes_ it punishment. If your people came here for my protection, the Others would stop me. Do you understand? I can never help your people." She started to walk away; John darted in front of her, blocking her escape.

"I'm not sure I'm gonna let you walk away that easily. And I'm not just talking personally here, although that's definitely part of it. There is so much more we can learn from you."

"I _can't_, John. The Others won't allow it. It's their highest law to never interfere. I am bound by those laws, however much I wish to help you."

"So, uh, we can never ..." He gestured vaguely, not quite sure what he was asking.

"I can never leave," she said gently.

"Well, I could come and visit --if you don't mind flirting with somebody from another species."

"Atlantis says you treat her well."

"Try to," he said with a shrug. "She gets a bit battered, sometimes."

"I meant the program."

"So did I."

Chaya smiled. "We're not as different as you think."

"I think we're more different than _you_ think," John retorted.

She bit her lip nervously. "I can show you."

"Show me?"

"By sharing each other. We will know each other as well as anyone ever can."

He thought about it for a moment before nodding. "OK. Gotta get the car back by midnight, though."

"This will only take a few moments." She gripped his arms lightly, raising them to rest on hers. Her fingers rested on the pulse point in his elbows. "Just close your eyes," she murmured, and as he obeyed he saw her begin to glow.

* * *

"That was fun," John said for the third time.

"I know," Alice agreed. "Keep the 'Jumper pointing towards the Stargate, John."

"Where're we going?"

"Back to Atlantis...did you actually let Chaya get you high?"

"I'm not high!" Conspiratorially, he added, "They don't let you do that in the Air Force. Makes it hard to fly."

"So I see," she said, watching the Stargate sail by on the right. "Ready to try again?"

"It keeps moving," he protested, starting the 'Jumper in a slow loop.

"I think you keep moving. Just point the 'Jumper at the 'Gate, and then stop pushing buttons, ok? And stop thinking," she added.

"I wasn't!"

The 'Gate sailed by on the left, this time, and she sighed. "John, we've done this six times now. Atlantis is going to be getting worried. Turn your radio on." John tapped at his ear, and she shook her head. "No, John. The big radio."

He found the radio after three false attempts, and Elizabeth's voice filled the cabin. "_...ard, can you hear us? This is Atlantis base calling Major Sheppard. Can you hear us?"_

" 'Lo, 'Lizabeth!" John called, grinning.

"_John?_" she asked hesitantly.

"Yeah. Hi!"

"_John, are you all right?"_

"Yeah! Everything's cool. Well, we can't go to Proculus anymore, and Chaya's an Ancient." To Alice, he added, "A People, right?" Elizabeth started to answer, but he continued, "So we can't go there, and she can't come to us, and we did this thing where we held hands and she went all glowy, and then she went away." Abruptly dejected, he sank back into the seat.

Behind Elizabeth, McKay hissed, _"He's on something!_"

Elizabeth shushed him before saying, "_John, the wormhole's been open for a while. Are you in trouble?"_

"It keeps moving," John explained earnestly.

"_I...see."_

"John," Alice said quietly, "We're pointing straight at the 'Gate now. Just go forward. Not in any other direction."

"What if we get stuck?" he protested.

"_I'm sorry, John, I didn't hear that," _Elizabeth said.

"Not you. I'm talking to Atlantis."

"_He's insane," _McKay said, horrified. _"He's actually insane."_

"_Rodney, hush," _Teyla said sharply. _"John? What is Atlantis saying?"_

"To go straight forward."

"_Then perhaps you should try,"_ she coaxed him. _"Atlantis helps you, yes?"_

"Yeah..."

"_Then listen to her, listen to _us,_ and come home."_

"Go," Alice said, and the 'Jumper shot forward and into the 'Gate.

* * *

"Major," Elizabeth said brightly, a day later. "Feeling better?"

John flinched, pressing back against his pillows. "Little headache."

"Sorry," she said, a little quieter. "Carson says your brain chemistry's back to normal."

"Is that what was wrong with me?"

"How much do you remember?" she asked, perching on the end of his bed.

"Not much. I remember saying goodbye to Chaya, but after that..." He made a 'poof' gesture. "Gone. How'd I get back here? Doc Beckett says I was pretty out of it."

"Atlantis called you," Elizabeth said, eyes dancing with laughter.

"Atlantis called me," he repeated, glancing towards the door. Alice had been lurking on and off since he'd woken, but they hadn't spoken and she wasn't there now.

"Yes, so you said. You had quite a conversation."

"I did, huh? Knew there was a reason I never did drugs. How'd I really get back?"

"You got the 'Jumper through. On your seventh attempt." She leaned forward to whisper, "The 'Gate kept moving."

"Tricky things, Stargates."

"Very," she agreed, rising to her feet and patting his leg. "Feel better."

"Thanks," he agreed, watching her leave. Alice slipped in before the door closed, hesitating just inside.

"You got me back?" he murmured.

"Mostly I said 'Fly to the right'," she said with a shrug. "Feeling better?"

"Much." He leaned back. "Who thinks I'm crazy?"

"Mostly everyone." She smiled suddenly. "Even knowing there's a mental component to the city's controls, none of them have even considered you were really talking to me. They all think it was an hallucination...except Teyla."

"Teyla isn't..."

"She hasn't told anyone."

"Good," John murmured, letting his eyes drift closed. "Hey...Alice?"

"Yes, John."

"Next time an Ancient comes to the city, warn me before they tell you to zip it, ok?"

"Yes, John." She sounded faintly amused, but he couldn't summon the energy to check. "Get some rest."

"Yes Ma'am," he mumbled, sliding into sleep.


	6. Before I Sleep

Author's note: Sorry for the delay. Once again, I don't own John, Atlantis, or anyone except Alice. I don't even own most of the words. Just for clarification, 'our' Elizabeth is Elizabeht, to ten thousand year old version is Weir.

Trecebo: Thanks! I quite liked that one myself.

Sharie: Glad you're enjoying. Hope you keep enjoying!

KansReader: You're welcome.

Kikide: I did love that scene. Poor Alice, she really has her work cut out for her with John, huh?

lakewater: Yeah, I liked that. Can't promise him high again in the near future, but I'll do my best, ok:)

Duchess67: Glad you like. Thanks for the review. :)

Before I Sleep

"This is a bad idea," John hissed.

"It's from your files," Alice said calmly. "People give presents to each other on their anniversaries."

"Yeah, but how'm I supposed to explain knowing her birthday?"

"Don't explain," she said with a shrug. "Your people almost never ask each other to clarify. It's odd."

John juggled the pack in his hands. "It's self defense when Rodney's talking. I still think this is a bad idea."

"It's not a bad idea. Who else is going to do it if you don't?"

"Yeah," John sighed. "All right. Wish me luck." Alice frowned and he shook his head. "Never mind."

"She's alone," she reminded him. "You wanted to know when she'd be alone. You've put this off three times now."

"This has to be planned, it's not like..."

"Fighting Wraith?" Alice said innocently. "Although you never seem to plan that either, so..."

"You, hush." He stepped forward, and the doors to the balcony obligingly parted.

"Hey," Elizabeth said, almost absently.

"There you are."

"I was just sneaking a breath of fresh air. Thought you were off exploring the city."

John gestured vaguely. "About to." He lifted his pack, pulling out the round parcel and handing it to her. "Picked this up on the mainland. The Athosians made it. Happy birthday."

"Hmm." Elizabeth carefully unwrapped the cloth and found a round pot. "It's beautiful. How did you find out?"

He carefully didn't look towards the door, where he knew Alice was lurking. "Mum's the word." He grinned innocently, heading back inside. Elizabeth studied the pot again, smiling to herself.

* * *

"Alright, we're done with the living quarters," John told his radio. "Moving on."

"_Woah-woah-woah-woah-woah-woah," _Rodney protested._ "Before you go. You see anything better than our current quarters?"_

"A few. Some of them are pretty nice, actually."

"_Well, what kind of square footage are we talking about?"_

"What am I, your realtor, Rodney? We're here to unlock the secrets of Atlantis."

"_Yeah, well, I'm looking for a one-bedroom with a den, preferably with a balcony, but I'm not married to it. Look ..."_

"Sir, check this out!" Ford called, momentarily drowning out Rodney's voice.

"_... we might as well be comfortable, at least until the Wraith get here."_

"Shut up for a second," John said absently. He and Teyla hurried to catch up with Ford, stepping into the room. The lights came on automatically as he came in, revealing a laboratory.

"_What? What is it?"_ Rodney asked.

"Some sort of laboratory," Teyla said, watching John prowl the room.

"_We've come across dozens of those. The city's full of them. Something unusual about it?"_

John ran a hand across one of the consoles. A capsule on the wall lit up, revealing an elderly woman.

"I'd have to say ... yes."

"John?" Alice called suddenly. He half-turned; she was out in the hall, peering in oddly.

He glanced at Teyla. "I'm gonna call Elizabeth and Carson. I'll be back in a minute." She nodded understanding, crossing to ask Ford about the capsule.

Alice spun when he stepped out into the corridor, looking unspeakably relieved. "John!"

"What?" he said softy, moving away from the door.

"Where were you?"

"I was in there." He gestured vaguely towards the lab.

Alice frowned, studying the door. "There's no there there, John. That's a wall. There's nothing on the other side, even."

"There's a lab in there!" John just about remembered to keep his voice down. "With a frozen woman, thank you. You're supposed to _tell_ me these things, remember?"

"There's nothing there!" Alice went back to the doors, leaning against thin air as though against a wall. "See?"

John studied her for a moment, "You really can't see it. Someone blocked it from the sensors." He tapped his radio. "McKay?"

"_Sheppard? Good. Where are you?"_

"I'm standing outside an Ancient lab, you and Weir and Beckett all need to come down here."

"_Why? The internal sensors don't show anything."_

"Really? Huh. Can you read Teyla and Ford right now?"

"_No," _Rodney admitted.

"So it's a _shielded _secret lab that you really need to see. Can you get Weir?"

"_Yes, yes, we're on our way."_

"Thank you." He tapped the radio off.

"What's in there?" Alice asked.

"A woman in stasis. A very _old_ woman in stasis. You sure you didn't know anything about this?"

"Nothing." Alice stared uncomfortably at the door. "There's nothing, John."

"I'm not going anywhere," he reminded her. Tapping his radio again, he added, "Carson?"

* * *

Teyla lingered when Elizabeth left the lab, watching John pace. "Well?"

"Atlantis can't see this room at all." John glanced back towards the corridor; Alice was standing outside the door, one hand pressed against the 'wall'. "She can't see us, she doesn't know anything about the woman, she didn't know this room was here."

"This room is blocked?"

"McKay couldn't see you and Ford, either. Don't think it's occurred to him to wonder why."

"He is a little preoccupied," she pointed out neutrally.

"Yeah." John halted, staring at the capsule. "Yeah, I know the feeling."

* * *

John had argued, hard, for them to transport the woman to the infirmary, but Carson was worried about unnecessary stress on her and insisted on using the lab. Unsurprisingly, it came prepared with everything they needed to revive her.

"Breathing shallow, pulse rapid," Carson mused, examining her. "I'll run an EEG to determine any brain activity." Turning away, he caught sight of a piece of paper in her hand. Tugging lightly, he freed it.

"What is it?" Elizabeth asked.

"Don't know." He passed the paper to Elizabeth.

"It's Gate addresses," Rodney said, reading over her shoulder. "Five of them. M7G-677 – we've been to this planet."

"Doctor Weir?" Teyla interrupted them. The woman was shifting, waking, and Elizabeth stepped closer to the bed, watching.

"Hello? Can you hear me?" she asked gently. The woman didn't react, staring straight ahead.

"Yeah, that's what I was afraid of." Rodney waved his hand in front of her eyes. "Freezer burn."

"I thought she wasn't frozen?" Ford protested.

"Ten thousand years," Beckett reminded them. "D'you expect her to dance a bloody jig?"

"It's the eyes, Carson, you look at the eyes. The lights are on but nobody's home. Don't take a medical professional to know that ..." He trailed off, watching her focus on him.

"Of course she can see us," Elizabeth said gently. "And hear us. Hello. How are you feeling?"

"It worked," the woman breathed.

"What was that?" Rodney demanded.

"She said, 'It worked.' " Elizabeth said absently.

"What's that mean?"

"I assume something worked," John told him.

"Yes, that's very sharp!"

"Thank you."

"Hello?" Elizabeth said suddenly, cutting across them. "She fell asleep." Glancing at Carson, she added, "Once you've got her more stable, transfer her to the Infirmary. And I want video on her at all times recording everything. We might not get a second chance at anything she may say."

"Let's hope we get a first, huh?" Rodney muttered.

* * *

John stretched absently, studying the screen in front of him. "Too big, huh?"

"I'm not saying it's too big, I'm just pointing out its dimensions," Rodney corrected him.

"Huh. It's not that..." He cut himself off when Elizabeth came in.

"Gentlemen."

"We were just wondering whether there were any other frozen bodies out there in Atlantis that we haven't discovered."

"There aren't," Alice muttered. John didn't look at her; Alice had been sulking since he'd left the shielded lab.

"And I was just saying there's no way of knowing in the short term. It'd be like searching every room in every building in Manhattan. It'll, uh, take a while. God knows what other kinds of surprises are out there not showing on the sensors."

"Well, that's what we're here to find out," Elizabeth started, but before she could continue her radio activated.

"_Doctor Weir_," Carson said.

"Yes?"

"_You'd better come to the Infirmary."_

"Is our patient awake?"

"_Aye – and she's saying the most peculiar things."_

"On our way." Elizabeth gestured the men out ahead of her.

* * *

Carson glanced up as they reached the infirmary, crossing to meet them near the door. Keeping his voice down, he murmured, "She's drifting in and out – still very weak. But there's something a wee bit odd about this woman. She called me Carson. She knows my name."

"Maybe she overheard you talking with someone," Rodney suggested.

"No. I was alone in here when she woke up."

"Well, what about subconsciously? I've read stories where coma patients have been able to hear..."

"No, no." He interrupted Elizabeth without seeming to notice. "It's more than that. She _knows_ things."

John lingered in the doorway as Carson led Elizabeth and Rodney to the bed. "Alice?"

"Yes."

"What's going on? How does she know Carson?"

"She's Elizabeth."

"What?" he hissed, barely remembering to lower his voice.

"Oh yes," the woman was saying, and he glanced over. "I'm you, Elizabeth."

"How is that..." His voice was unexpectedly loud in the quiet room, and Rodney and Carson glanced at him. "Sorry," he muttered, taking a couple of steps back.

"Carson hasn't tested her DNA yet," Alice said quietly, "but when he does, it'll match."

"Your scanners read DNA?" he demanded.

"In here they do. They're both Elizabeth Weir. But one is ten thousand years old."

"Ten..." Looking up, he caught Rodney's eye and demanded, "Time travel?"

* * *

"That's what she said," Elizabeth said later. "She somehow found a way to travel back in time to when the Ancients inhabited the city."

"How did she do this?" Teyla asked.

"That will be one of the first questions I ask her when she wakes up again."

"_If_ she ever wakes up again," John muttered.

"Well, let's not be too quick to exclude the possibility that the woman might be, umm, what _is_ the clinical term ... nuts?" Rodney, to give him credit, looked mildly discomforted at the idea.

"She may be senile, yes," Elizabeth agreed, "but that doesn't explain that she knows so much about all of us."

"Is time travel even possible?" Ford asked.

"Well, according to Einstein's General Theory of Relativity, there's nothing in the laws of physics to prevent it. Extremely difficult to achieve, mind you – you need the technology to manipulate black holes to create wormholes not only through points in space but time."

"Not to mention a really nice DeLorean." John cut him off before he could start explaining wormhole physics.

"Don't even get me started on that movie!"

"I liked that movie."

Carson came in, passing a computer pad to Elizabeth. "The results of the DNA test. It's a match. She _is_ you."

"Told you," Alice reminded John. "And your computer records say that teams from your SGC have time traveled before. In both directions."

"McKay, what do you know about time travel?" John asked. Rodney started to answer, and he added, "Short version."

"It's possible. SG1 have traveled into both past and future, although that involved an odd combination of sunspots and wormholes."

"So she's not, say, from another dimension? Shapeshifter? Alien impersonator of some kind?"

"Entropic cascade failure," Alice murmured.

"She's not an alien," Carson said firmly.

"She's definitely been in that capsule for ten thousand years, so she's hardly an imposter. And if she were from another dimension we'd be seeing entropic cascade failure by now."

John slanted a glance at Alice, who was smiling contentedly. "Show-off," he muttered. Louder, he added, "So she's really Elizabeth Weir? From Earth?"

"She is," Carson agreed.

John glanced at Elizabeth, who was staring blindly at the pot on her desk. "Well, call us when she wakes up again. McKay, why don't you go poke around the tube some more? See if it's got a log, or anything?"

"I must also go," Teyla agreed, turning to Ford. "You promised to show me that move, Aidan, remember?"

"Uh...sure, Teyla," Ford agreed, letting her usher him out of the room.

John and Carson had a brief, silent conversation before Carson capitulated and left them alone. John shifted out of his seat, perching on the side of her desk. "Elizabeth?"

"Ten thousand years," she said reflectively. "It's a long time to sleep."

"You—she must have had a reason."

"Yes, I suppose so."

"Eliz..."

"Don't you have some security to check on?" she said too fast, cutting him off.

"Yeah," he said slowly, studying her. "I'll go do that." He tapped the desk in front of her, catching her attention. "Call me if you need me."

"I'm alright, John. Just...need to take it in."

"Alright," he echoed, sliding off the desk.

Outside he murmured to Alice, "Turn off whatever scanners you can. Let her have some privacy."

"I can't turn them off," Alice said, "but I'll bury the feed so no one will find it."

"That'll do. Thanks."

* * *

Much later John slipped into the infirmary, watching Elizabeth watch Weir. So far, the story made a sick kind of sense, but telling it was draining Weir faster than any of them would have believed.

"How's she doin'?" he asked quietly.

"Stabilised but still very weak – and getting weaker."

"Your own mortality staring you right in the face. I can't imagine how you must be feeling."

"When she looks at me, it's as if she's sensing my thoughts, and I'm sensing hers. It's _very_ unsettling."

John shifted uncomfortably. "Just when you thought this place couldn't get any weirder," he offered.

Rodney came in, glancing from one to the other.

"Well, it's obvious. The Puddlejumper they escaped in must have been some sort of a time machine; had to have an additional component built into it."

"Flux capacitor!" John said, grinning.

"... Yeah." Rodney immediately dismissed him, turning to Elizabeth. "The question is, where's the time machine now, hmm?"

"Why don't we ask her?" Elizabeth suggested. John took a couple of steps closer, watching Weir open her eyes.

"What happened?" she asked.

"Can you tell us: the ship that you escaped in – where is it now?" Elizabeth asked.

"It's gone," Weir said quietly. "We flew into a fight, we didn't know who anyone was...there was an explosion. The next thing I knew, I woke up here."

"You mean now?" John asked.

"No. Then." Her gaze was distant. "There was an Ancient there; his name was Janus. He healed my wounds and explained to me what had happened...that the 'Jumper had gone down. Only I survived."

"Ha!" Rodney said happily. "Ah, the bitter taste of ultimate failure, hmm?" He grinned at John.

"Well, if you'd just figured out how to fix the damn shield in the _first_ place, none of us would have died," John reminded him.

Weir and Elizabeth exchanged rueful grins when Rodney protested, "I did everything I could, including _valiantly_ attempting to save your sorry..."

"Gentlemen," Elizabeth said sharply. "Focus. Please, continue."

"Needless to say, I was very confused," Weir went on. "He explained to me that the ship we had escaped in was a time machine. He was the one who built it. After I was feeling better, he brought me before the Atlantean Council." Her gaze shifted again. "They told me of beings called Wraiths – a vicious, formidable enemy whose power and technology rivalled their own."

"Yes – actually, we've already, umm..." Rodney trailed off uncertainly.

Weir didn't seem to hear him, continuing, "The Atlanteans sent a delegation protected by their most powerful warships in the faint hope of negotiating a truce. One on one, the Atlantean ships were more powerful, but the Wraith were so many. After that great battle, it was only a matter of time. They were preparing to leave, to retreat to Earth."

"You didn't go?" Elizabeth asked.

"I wanted to come home. Here." She glanced around the room. "They refused. Too damaging to causality. They ordered the 'Jumper destroyed, and I was to return to Earth with them."

Carson came in, catching Elizabeth's eye, and she excused herself. John wandered into the furthest corner, out of Rodney's hearing.

"Alice?"

"Yes, John," she said from behind him.

He didn't jump, but it took almost everything he had. "Don't do that," he hissed.

"Sorry, John."

"You didn't tell me Elizabeth was on Atlantis before!"

She blinked. "Was she?"

"Haven't you been listening?"

"Privacy for Dr Weir. All the recordings are being buried...you _told_ me to do it."

"I didn't tell...I did tell you to do that. Alright. Stop doing it now. Can you retrieve the last five minutes?"

Alice glanced away. "I wasn't online."

"When?"

"Ten thousand years ago. I'd been turned off by the time Dr Weir arrived."

"Turned off?"

"Information retrieval and problem solving," she reminded him. "There wasn't any need for me, everything was shut down. All the research." Glancing over his shoulder, she added, "You're wanted."

John turned to see Rodney trying to catch his eye. As soon as he joined them, Carson started listing the things that were wrong with Weir.

"How long does she have?" John asked, cutting through a list that he, sadly, mostly understood.

"I doubt she'll live out the night," Carson admitted.

"Please," Weir breathed. "I don't know how much time I have left to tell the story I have waited so long to tell. Oh ... the Council. They were very upset."

"Yes – you said they decided to destroy the time machine," Elizabeth prompted her.

"I tried to talk them out of it. I didn't give up hope. Thankfully, I had an ally. Janus fought to get me home, used up all his favors, anything he was owed. All for nothing; no one would listen. I would go to Earth, the city would sleep, and in ten thousand years it would happen again."

John glanced at Alice, who was visibly upset; before he could do anything about it, Weir was continuing.

"Of course, Janus refused to concede defeat. The more someone told him not to do something, the more he had to do it. So he came up with an alternate plan behind the Council's back. It was all I could do to try to keep pace with him." She smiled faintly. "Like listening to Rodney explain something."

"Uh—thanks?" he said uncertainly.

"He planned to have the city use only one ZPM at a time, to extend their lives. He showed me... I didn't believe my eyes. Three ZPMs right in front of me. His plan had a hitch, though; the ZPMs needed to be physically switched during the ten thousand years."

Elizabeth's eyes widened and she glanced at John. "That's why..." he muttered, but Weir was still talking.

"Their transport ship was inbound. It was taking heavy fire. The pilot couldn't..." She tossed fretfully, and Carson hurried forward.

"Easy," he murmured. "Relax, love."

"Carson..." She smiled. "I missed you." She drifted back towards sleep, and Carson straightened, sighing.

* * *

It was late that night before Weir woke again. Rodney and John had both dozed off, but Elizabeth had been unable to sleep. She was sitting by Weir's bed, absently stroking her hair.

"Damn," Weir murmured. "Fell asleep again!"

"Well, you're not the only one," Elizabeth assured her, glancing at Rodney and John. "Are you in any pain?"

"Would we admit it if we were?"

"I wish there was more we could do for you."

"Oh, _look_ at you! Always worrying. You put too much pressure on yourself. Remember that miserable Baltic negotiation? What Simon told us afterwards?"

" "Breathe" – among other things!" Elizabeth smiled.

"John," Alice said, loudly enough to wake him. "Don't move," she added quickly. "But I think this is it. She won't wake again."

"Enjoy the moment – what's here right now," Weir continued. "The sun, the breeze ... our birthday!"

"Sheppard couldn't keep it to himself, huh?" Elizabeth said wryly.

"I'm just saying stop being so damned hard on yourself. Life is quick."

"Not for you," she said softly.

"It was my choice, Elizabeth. I didn't second-guess it then, and I don't regret it now. Janus told them I'd gone already. But I was getting ready to sleep. Janus prepared the stasis chamber for me – said it would be like a deep, dreamless sleep. I would wake three times, twice to turn the ZPMs, once to greet you. He programmed a failsafe as well."

"The rising," Elizabeth agreed.

"The rising. The city would rise to save you, if I couldn't. And then they left – all of them; returning to Earth through the Stargate. And then I was alone. I set the city to slumber...and began my long journey home."

"It worked," Elizabeth said quietly. "The stasis, the failsafes. You gave up your entire life."

"No – because we are the same person. The best part of my life – it's just beginning. I'm exploring a new galaxy. I have years ahead of me still. Trust yourself, Elizabeth. All that matters is right now. And the note – I wrote it in case I didn't survive. Has Rodney figured it out yet?"

Elizabeth shook her head. "Five Gate addresses."

"Outposts," Weir corrected her. "Each one with a Zero Point Module. Janus told me."

Elizabeth rose, moving to wake John and Rodney. "The note she left – coordinates of planets to have known ZPMs."

Rodney pulled the note from his pocket; John plucked it from his fingers. "They could still be there."

"M7G-677's on here! I mean, this is amazing! Elizabeth, we've got..."

"John," Alice said quietly. Rodney had already stopped talking, realizing Weir's heart monitor was flat lining. Elizabeth crossed to the bed, reaching to hold her older self's hand.

"I liked Janus," Alice said reflectively. "He was a good man."

"Not the time," John muttered. She nodded, turning away.

* * *

"Do you have privacy settings?" John asked idly.

"I don't go in your quarters," she said with a shrug. "The People didn't program me for privacy—if they didn't want me, they turned me off."

"Can I program you?"

"I'm self-programming. Tell me what you want."

"I want you to bury anything you're recording of Elizabeth when she's alone."

"For how long?"

"Until I tell you to stop. Can you do that? Bury them so no one will find them?"

"Of course I can."

"So Rodney won't fall over them?"

"Even him. Trust me."

"I do." He glanced around. "She alone?"

"Has been since the last time you asked."

"What's she doing?"

"Privacy," Alice reminded him, and he made a face.

"Yes, fine." He headed for the balcony.

Outside Elizabeth was slowly fitting the lid back onto the small round pot. John stepped close enough to the edge to see the cloud of ash still drifting down, but he was careful not to comment.

"We're about to start our mission briefing, so..."

"I'll be right there," Elizabeth agreed. John hesitated, about to say something, but changed his mind, heading back for the door. Just as it opened, she added, "Actually, John—give me a minute, will you?"

"Sure," John agreed easily, heading back in and letting the door slide closed behind him.


	7. Letters from Pegasus

Author's note: The things in this fic that aren't mine include characters, settings, plots and most of the words.

Duchess: I'd like to read yours. Let me know. :)

Trecebo: Thanks! I'm doing my best to make it so if you didn't really know, you wouldn't know which bits I stole and which ones I made up...glad to know it's working at least so far. :D

* * *

**Previously on **_**Atlantis**:_ Long range scanners detected three Hives on their way to Atlantis. ETA: two weeks.

Letters From Pegasus

"Well, we knew they were coming; at least now we know when." Elizabeth stared at her hands, clasped together on the table.

"That's something," John agreed.

"That's something?" Rodney repeated disbelievingly.

"It means there's still time, Rodney—there's no reason to panic...yet."

Alice, prowling the edges of the room, glared at him for that.

"Where there is time, there is hope," Teyla said placidly.

"Agreed. So, recommendations?" Elizabeth looked around at the group.

"Other than panic?" Carson muttered.

"Other than panic, yes."

"I realise this might not be cool," Ford said hesitantly, "but we should consider M7G-677."

"As a possible evacuation site?"

"No, ma'am. I'm suggesting we take their ZPM."

"Their only means of protection from the Wraith?" Elizabeth said pointedly. "A planet populated mostly by children?"

"He raises a valid point," McKay said thoughtfully. "We've already established that the ZPM is nearly depleted, but it could be of some limited use to us."

"You asked for suggestions," Ford reminded her. "It's a matter of survival."

"I see. Well, we're not quite there yet, and as long as I'm in charge, we will never be there."

"I agree, Doctor Weir. If this is to be our end, it is best we face it with both dignity and honor." Teyla even managed not to sound accusatory.

"To that end, I actually have an idea – in addition to panic." Rodney looked even more proud of himself than usual.

"Let's hear it," John prompted him.

"It's really a long shot, but I think it's, uh, most likely worth the effort. Of course, it will mostly be my effort, so..."

"What is it?"

"I think we can send a message back to Earth through the Stargate."

"Excuse me?" Carson's exclamation was mostly overruled by Weir's, "I thought we didn't have enough power."

"Not to send a person, no," Rodney said. "We'd never be able to maintain the wormhole long enough. But I think if we were able to tie together all of our power-generating capabilities, we might – and I emphasize might – be able to establish a wormhole long enough to send a message."

"How much time are we talking about?" John asked.

"Well, approximately, uh, one point three seconds, give or take."

"That's not much time," Carson said dubiously.

"Time enough to say, 'SOS' " Ford muttered.

"Don't be so analogue!" Rodney protested. "One point three seconds is more than enough time to send a message if it's in the form of a high compression data burst. Now, I helped refine the encoding for the US Air Force a few years back. Colonel Carter should be able to, uh, decipher it on the other side."

"You're suggesting this now?" John asked.

"Because it probably won't work, and there's a very good chance it could overload our naqahdah generators in the process."

"Well, then, we can't take the risk! No power, we won't have a chance in hell!"

"There are _three_ Wraith hive ships on the way, Major! Desperate times call for desperate measures. Besides, I spent the last few days working out ways of minimising the risk."

Elizabeth cut between them. "Assuming it's possible, how much information could we send?"

"Everything. I mean, uh, mission reports from all the senior staff, uh, a ton of stuff on Atlantis, things we've learned in Pegasus..."

"All that, one second?" Ford said in surprise.

"One point three," John reminded him semi-seriously.

"See, you jest, but if I can finesse the compression ratios, you'll be looking for things to add."

"Do it," Elizabeth said.

"Doing it," Rodney agreed, leaving. The others followed him; John followed Elizabeth through the Control room towards her office.

"Elizabeth. You realise that if Stargate Command was able to send help..."

"I know. They would have – but still, we have a responsibility to report what we've learned here, about Atlantis, about the Ancients..."

"...the Wraith," he finished.

"Exactly. We have to warn Earth."

"Even if it's the last thing we do?"

"Especially if it's the last thing we do."

John nodded, peeling off and heading for one of the corridors. The city was unusually busy, everyone aware of the oncoming ships, and eventually he took a transporter to an empty sector.

"There's nothing helpful here," Alice told him.

"I was looking for you. Rodney's plan. Will it work?"

"His program works," she said carefully. "The information will be small enough. I don't know about the power. The Stargate was designed to run on a ZPM. Your generators are fine for what you ask of them, but to dial your galaxy..." She shrugged helplessly. "I don't know."

"Keep an eye on him. Let me know if anything goes wrong." Alice nodded, and he considered her for a moment. "How are you doing?"

"If the Wraith take Atlantis, every bit of information in the computers, all over the City, will be wiped. They'll get a husk. Less than that; none of the machinery will function. Nothing."

"Are you telling me or warning me?" John wondered.

"It's hardwired into every system. If they come I will kill the City, and I will die. They will not get to Earth this way."

He thought about that for a moment, deciding to take it in the spirit it was apparently offered. "Thank you."

His radio crackled to life before she could answer. _"Major Sheppard?"_

"Yeah, Teyla."

"_You are needed in Control."_

"I'm on my way." He turned the radio off, heading for the transporter. "Coming?"

"I'll meet you there," Alice told him.

* * *

In command John stood with Elizabeth and Teyla, watching the screen over Zelenka's shoulder.

"They don't seem threatening as dots on the screen, do they?" Elizabeth said wistfully.

"Which is why we need to do recon and see what we're up against first hand," John agreed.

"How?"

Zelenka gestured to the screen. "I've been tracking their progress. The Wraith ships apparently go in and out of hyperspace periodically – either because their hyperspace technology is limited..."

"...or they're stopping to feed along the way," John muttered.

"The point is, the pattern is predictable. I can guess with some certainty that they'll be making stops here, here and here." He pointed out the places on the screen.

"Even so, those ships are light years away. How do you expect to reach them in a Puddlejumper?" Elizabeth protested.

"We fly to a Stargate en route that Zelenka thinks they're gonna drop out of hyperspace and we watch 'em pass by," John explained.

"That's good."

"Well, I have my moments. Teyla and I were just deciding which planet to go to."

"I am familiar with the people of this world." She gestured to the screen. "Their Stargate is in the open and so accessible by ship."

"And you think you can remain undetected by the Wraith as they go by your position?" Elizabeth asked.

"Stealth mode," John reminded her. "They won't even know we're there."

"OK," she agreed. "Go. Get what intel you can and get back – _before_ Rodney sends his message. I need the both of you here."

"Won't even stop at the duty free," John promised. He and Teyla headed off.

* * *

"_On the off-chance you decide to take the Wraith ships on yourself, Major,_" Elizabeth said over his radio, "_I am hereby ordering you not to."_

John was mostly concentrating on the 'Jumper, but he spared enough attention to tell her, "Believe me, you don't have to."

"_Still_..." Elizabeh let it trail off.

"...don't take on an alien armada single-handed. Understood!" 

Teyla glanced around as they reached the other side of the wormhole. "Are we alone?"

John glanced over his shoulder; Alice held both hands up innocently and vanished. "We are now."

"She follows you?"

"She likes the 'Jumpers," John said innocently.

"She likes you."

"She's a program, she doesn't _like_ anything."

Teyla eyed him, wondering if he really believed that, but she decided to ignore it for now. "I have spoken with Halling," she said instead. "We feel that perhaps the Athosians should be evacuated."

"We're keeping it in mind," John promised. "We won't leave your people in trouble, Teyla."

"Does Atlantis believe she can stand against the Wraith?"

"Not sure. She's already promised to trash the city if it comes to it, though."

Teyla shifted. "She can do that?"

"Wipe the computers, burn out the operating systems," John said easily.

"She would destroy herself?"

"To protect the city and the expedition, yeah." John glanced at his HUD. "Is that your friend's village?"

"Yes." Teyla studied the display. "The village has grown."

"Good. Al—Atlantis."

Alice stepped out of the rear compartment. "Yes, Jo...Major."

"Definitely too much time in Rodney's systems," he muttered. "We're landing here. Watch the sensors and warn me if the Hives come."

"You already know they're coming," she pointed out.

"_Ahead of schedule," _John said semi-patiently. Catching Teyla's look, he added, "What?"

"She thinks it's funny you're arguing with yourself," Alice said blandly.

Overlapping, Teyla said, "Watching you argue with no one is...interesting." Glancing over her shoulder, she added, "No offence intended."

"I'm not programmed to take offence," Alice said politely.

"You're forgiven," John told Teyla. "Keep an eye out," he added to Alice, pushing away from the console.

"Always do," she reminded him.

* * *

John had set down near the fields, and it was only a few minutes before they were recognized. "Father! Teyla's here!"

John glanced up at the call to see a young boy running towards an older man. Teyla smiled, waving, and both returned the gesture.

"Teyla!"

"Orin! It has been many days."

"Too many!" Orin had reached them by now; he and Teyla touched foreheads. "Look at you! You're so different!"

"Much has changed since my last visit. This is Major John Sheppard – and Orin."

"Pleased to meet you," John said politely. He offered a hand, but Orin was already saluting him, hand on his heart. John mimicked the gesture a little more awkwardly.

Orin smiled vaguely and turned to Teyla. "The harvest is still several months away."

"Yes, I know. We have not come to trade, but to deliver a warning. We have reason to believe the Wraith may be on their way."

Behind Orin, the other villagers began to protest, and John added quickly, "We don't know that for a fact but we're about to go and find out."

"Yes," Orin agreed grimly. "It seems they are awakening everywhere."

"You should tell your people to take precautions in case they do come," Teyla told him.

"I will – but you know as well as I do, Teyla, that the Wraith will track us down wherever we go. There will be no escape."

"What about through the Stargate?" John asked.

"The cullings are taking place on many worlds. None are safe. Even we have taken in refugees." He glanced down at a boy leaning against his hip; his meaning was clear, and Teyla nodded.

"If they do come, stay far from the Stargate. Take your family to the far tree line, there, and wait for us."

"Teyla..." John said warningly.

"One family, Major, that is all I ask."

John looked around at the group, then back at Orin. "I'm sorry, Orin, I can't make that promise."

"It will be the very least we can do," Teyla said, directly to John this time. Giving up, he gestured vaguely.

"If there's time."

"Then we must hurry." Teyla leaned her forehead against Orin's again and then led John back towards the 'Jumper. Behind them, John could hear Orin call for the village to begin preparations.

* * *

John managed to hold back until they were back in orbit. Teyla waited him out, sitting silent in the copilot's seat.

"This wasn't supposed to be a rescue mission." John flipped on the cloak, not looking at her.

"Orin was a good friend of my father."

"I agreed to _warn_ him."

"If someone close to your family – a dear friend – was in danger of being taken by the Wraith, would you have not done the same?"

"Not if it jeopardized the mission."

"So in fighting the Wraith, we are to give up that which makes us different from them?"

"She's good," Alice said admiringly. John rolled his eyes at her.

"I agreed to stop and pick him up _if_ there was time – but _only_ if there was time. I could be saving everyone in the damned galaxy if we could."

"One man and his children are not every person."

"I agreed to help if there was time. You can only fight the battles you can win."

"John," Alice said warningly, cutting him off. She leaned between them, gesturing to the viewscreen.

"Woah!"

He managed not to duck as two Hives emerged from hyperspace and flew directly overhead. A moment later another joined it, and Darts began to swarm around them.

"I'll get this thing turned around," John muttered.

"They are heading for the planet," Teyla said sharply.

"Aw, _damn._ Alice, get the display up...no, smaller. I need to see the Hives and the planet."

"It won't be any good to you that small," Alice protested, but the HUD came up anyway.

"They are definitely going to the planet," John muttered. The 'Jumper spun, going from a standstill to almost full speed.

"That's going to hurt later," Alice said.

"I'll have Zelenka check you out," John promised. They hit atmosphere and he slowed a little, watching the display. "Sorry, Teyla. Even flying full out we're just ahead of the armada. I can't risk putting down for Orin or his family."

"I see," Teyla said neutrally.

"I'm gonna take us out of stealth mode for the pass through. Dial the Gate."

Teyla hesitated for a moment before beginning to dial. Halfway through the sequence an alarm went off.

"Hang on! Incoming wormhole!" John yanked the 'Jumper into a tight curve, pulling them hard away.

"I have heard stories of the Wraith dialing in to prevent their victims from using the Stargate as a means of escape," Teyla said thoughtfully.

"Takes some timing," Alice muttered.

"So we're stuck here," John clarified.

"Once the ship is rendered invisible again, we will be perfectly safe."

"I'm worried about getting the intel about the Wraith fleet back to Atlantis."

"They will keep dialing in through the night at the very least – but if we wait in the location I told Orin and his family to meet us..."

"That's where I'm headed," John said with a sigh.

"Orin's family?" Alice repeated.

"Teyla's contact. We promised we'd try to swing back for them," John told her. Catching Teyla's look, he added, "Atlantis was wondering."

"There's a landing spot there," Alice offered, gesturing. The HUD flashed once before returning to the view of the system.

"No. In the tree line. That's where Orin will be looking for us."

"Landing's harder in the trees," Alice mused. "There." The HUD flashed again.

"Is that not distracting?" Teyla asked.

"No." John glanced up; the HUD obligingly flashed the landing spot again. "It's not."

The HUD vanished as the 'Jumper landed; John glanced out, gauging the sky. "It's dark already."

"The days are short here."

"18.3—"

"Thanks, Alice, good enough." John pulled his binoculars out of his pack, scanning what he could see of the village. "C'mon, Orin, show up!" He dropped the binoculars, drumming on the control panel until he realized Teyla was staring at him. "What?"

"Not long ago you would have blithely left him behind."

"Well, the situation has changed."

"Earlier today Lieutenant Ford suggested we steal from a community of children."

"It's because they have a ZPM and we can bring them back."

"Only to face death in Atlantis?"

John took a deep breath. "Look, Ford and I are military. We've spent a lot of our lives learning how to survive."

"I have spent my life surviving the Wraith."

"Part of that training," he continued doggedly, "is knowing who you can save and who you can't."

"And that decision is yours alone?"

"I _said_ that I'd wait for your friend if there was time. Now there's time. What else do you want from me?"

"Too much, I fear." Teyla turned away, heading into the rear compartment. Alice crammed herself against the wall to avoid her, glancing almost timidly at John.

"It's gonna be a long night...Don't say it," he ordered her.

"What would you like me not to say?"

"I would like you not to say..." He hesitated, thinking the sentence through. "Never mind. What do your scanners say?"

"Darts. No Wraith on the ground yet, though."

"That's one good thing," he muttered. He tensed as a Dart flew overhead, transporter beam flaring as it crossed the village.

Teyla slipped back up by his side, watching with him as the Darts continued to criss-cross the village. "This is hard to sit and watch," he said quietly.

"There's nothing we can do," Teyla said wearily.

"We _could_ do a lot. It'd just be the last thing we'd ever do."

"We are far outnumbered and the Gate is still inaccessible." She glanced at him. "But if we save Orin and his family, we will have done something."

"Something," John echoed vaguely.

"Gate's shut off," Alice commented. "No...it's dialed back in."

"You can stop reporting that unless it doesn't redial," John told her.

Alice tensed suddenly, eyes flickering. "John..."

She cut herself off as a solid white beam shot up into the sky from the village. John swore softly, staring at it.

"What is that?" he demanded.

Teyla shook her head. "I have never seen such a thing."

"No references in the database," Alice added quietly.

"I'll go and check it out." He headed for the rear compartment; Teyla caught his arm, stopping him.

"You may be discovered," she warned him.

"I'll make a point not to."

"Major..."

"I just wanna see what...whatever that is. Just stay here until Orin and his family show up."

He clipped his P90 on, slipping out as the 'Jumper opened. Teyla waited for him to walk past the front of the little ship, heading for the village.

He faded from sight quickly, and Teyla stepped into the back of the 'Jumper, aimlessly shifting kit from one pocket to another. "Atlantis," she said as though to herself. "Do you watch him?"

The HUD flashed up, showing a scan of the life signs in the village. One blinked as she watched.

"That is the major?" It blinked again, steadily, and she smiled faintly. "Thank you."

The HUD switched off again and Teyla went back to aimlessly moving the kit. The noise of the Darts rose outside; she gritted her teeth, deliberately not looking at the viewscreen.

Suddenly she stopped, thinking, and then turned slowly towards the back of the 'Jumper. John had left the ramp open and she had a narrow view of the clearing...enough to see a Wraith wander into view. It looked puzzled; Teyla held her breath, morbidly sure it could see her through the cloak.

It wandered around the clearing for a minute, coming in and out of her view; she eyed her gun, lying on one of the benches, but she was afraid to move for it in case the Wraith heard her. The cloak blocked sight, not sound, and she was very aware of how close the scout was.

It turned away, eventually, unable to find her, and she relaxed, sighing. The lights flickered once and she smiled ruefully. "Yes, that was too close," she agreed softly.

* * *

When she'd moved all the kit twice, she finally gave up and went back to the cockpit. The HUD periodically showed John's life signs, but it stayed off most of the time, letting her watch through the viewscreen.

Figures moving through the woods caught her attention and she rose to her feet, studying them. Two men, and a women with a child...not figures she recognized, but that hardly mattered.

She flicked the cloak off, stepping onto the ramp so they could see her. "Over here! It is alright – I am a friend! Please! Hurry! This way! Hurry! This way." As soon as they were inside she put the cloak back on. 

She glanced out the screen to be sure no one else was coming before turning back to one of the men. "How many of you remain?"

He shook his head, exhausted. "I don't know. The Wraith are everywhere."

Teyla found a water bottle, offering it to the woman. "Here – drink this. It is water." To the man, she added, "Orin? Have you seen him?"

"Not since before the Wraith arrived...Thank you." He drank form the bottle she was offering him. "We must go now – the Wraith will find us."

He started to leave, but Teyla stopped him. "No they will not. Our ship has a shield which makes it invisible to them. You are safe here. Just rest. We will leave soon."

The man hesitated, but she was able to urge him to sit with his friends. Making sure they were all as comfortable as she could make them, she retreated back to the cockpit, picking up John's binoculars to watch the tree line.

It was some time before John appeared, running towards them. Teyla dropped the binoculars, threading her way between the refuges to stand on the ramp, guiding John in. 

"Major!"

"It's pretty ugly out there. Is this Orin's family?"

"No. They have not seen Orin since the culling began."

"The village is pretty much wiped out." He slipped past her, picking up the binoculars and looking through the viewscreen. "The Gate just shut off. We should be able to dial up and get out of here before the Wraith can do anything about it."

Teyla stepped into the cockpit, watching him. "Please, Major – give Orin more time."

"If he was able to get here, he'd be here by now. We've gotta get back."

"Then go. I will stay and search in the daylight. You can return for me later."

John shook his head. "Can't do that."

"I consider Orin as family, Major. I am sorry if you do not understand what that means."

"I understand it, Teyla, but that's not the point."

"With or without you, I am staying."

He studied her for a moment. "You won't make it."

"Then I ask that you stay as well – just a little longer. Allow something good to come of this."

"Alright. We'll give him a little more time."

"The Darts are leaving," Alice offered. "The Wraith on the ground are almost gone. Attack's about over."

"Good," he said absently.

"What was the beam?"

"What?"

"The beam. The white beam. The one you went to look at."

"Oh. No clue." He passed the binoculars to Teyla. "Someone's coming."

Teyla glanced through them, smiling, and grabbed her P90, following him out of the 'Jumper. "Orin! Orin!"

"How big is his family!" John asked.

"He must have met up with others along the way." Orin was leading several people...she counted six without even trying.

"That's gonna be a problem."

"I didn't think you'd still be here," Orin gasped when he reached them.

"We would not have gone without you," Teyla said soothingly, glancing over his group.

"We found others on the way," Orin explained, "and even more further behind."

"How many more?" John demanded.

"Uh, twelve – perhaps more."

The second group were now visible, running for the 'Jumper. One of the men already in the ship stepped onto the ramp, marking it for them. "In here! This way! Quickly!"

"Wait!" John protested.

Anything else he might had said was interrupted as two Darts flew overhead. John ducked automatically, watching them circle to come back. "Alright, we'll fit as many people as we can!"

"Hurry! Come on!" Teyla ordered, pushing Orin towards the 'Jumper.

John snatched up a child, carrying her towards the ship as the Darts flew by again. A transporter beam ranged through the group, sweeping several people away; John dived for the ramp, crashing onto it with the girl still in his arms.

The group still outside were too late; the second Dart swept them up. Orin began to cry, holding another of the children.

John sat in silence for a moment before climbing to his feet, handing the girl off to another man before heading to the cockpit. Alice was sitting in Teyla's seat; she didn't speak as he powered up, dialing the Gate for Atlantis.

Teyla settled the refuges as best she could and came to join John, staring at the remains of the village as the 'Jumper passed over it.

* * *

Once they were through the Gate Alice straightened, standing just behind John. "No change, Hives still on course. The message is almost ready; Rodney's compressed it, so there's all your logs, a lot of things they've deciphered from my databanks, personal messages from the expedition...the power's fine. It won't drain the ZPM."

John nodded absently, glancing back at the refuges. "Welcome to Atlantis, everyone. Just stay where you are for a few minutes, we're gonna get the medstaff up here to check you over, ok?"

Teyla was already on the radio, calling the infirmary and assuring Elizabeth that both she and John were fine. Carson's medics were waiting when the 'Jumper docked, and they rapidly decided no one was seriously injured. John and Teyla quietly absented themselves, joining Rodney in the conference room.

Elizabeth came in a couple of minutes later. "Are our guests comfortably settled in?"

"Yes."

"Good. So tell me..." She took a deep breath. "How bad is it?"

"Bad," John said bluntly. "Each hive ship acts like a carrier group with cruisers and hundreds of Darts escorting it. Grodin's downloading the sensor readings right now."

"I have never witnessed a culling that took so many," Teyla agreed.

"We saved a few – that's worth something."

Elizabeth looked at Rodney. "Rodney, are we ready to send our message?"

"When you are."

"OK."

Rodney and Teyla left, but Elizabeth held John back. "Lieutenant Ford is just finishing recording the personal messages from all the team members. If you'd like..."

He shook his head. "I'm good."

"OK. Well, then, along with a short note of my own, I took the liberty of recording messages to the families of the people we've lost."

"It's a good idea."

"But there's one in particular I thought maybe you'd like to do yourself."

John took a deep breath. "Sumner."

"If you want to."

"Yeah. I'll take care of it."

* * *

A little later Rodney stuck his head into Elizabeth's office. "We're ready when you are."

Most of the city had managed to find a reason to be in the 'Gate room; Elizabeth smiled faintly, turning to Grodin. "Dial Earth, please."

It was fairly anti-climatic; as Rodney had predicted, the wormhole was only open for just over a second, barely enough to register. Rodney watched the power levels, nodding in satisfaction.

"We still have more than enough to protect the city," he announced.

"And the messages?" John asked.

"They reached Earth safely."

Everyone drifted away; John left Rodney still explaining the brilliance of his message compression programme and chased Teyla. "Teyla, wait up."

"I wish to speak with Orin and make sure he is well." She didn't look at him as she spoke.

"Just wait a second, would you? I wanna apologize!"

"There is no need." She did finally stop, turning to face him. "I understand your reasoning."

"I would have found a way to help him."

"I believe you." She sighed, taking a step closer. "I understand, John. I have made such decisions. Now I must go and see Orin. I will see you soon."

She turned away, heading for the infirmary; Alice stepped out of the nearest door as she passed, watching her vanish. "She worried for you while you were gone," she offered.

"I worried for me while I was gone, too," he retorted. "How much power is left in the ZPM?"

"Not much. Shields, drones. Life support, for a while. I'd start shutting down all unnecessary programs, if I were you."

"You stay online," he said quickly. "I need you."

"Yes, John."

"Warn me when the Hives reach the system, ok? Wherever I am."

"In your quarters?"

"Yes, in my quarters. Anywhere. Understood?"

"Understood. John?" she added as he turned away.

"Yes."

"You didn't send a message home."

"There's no one waiting for me."

Alice shook her head. "I know your personal file, remember. Father, brother, ex-wife."

"There's no one waiting for me," he repeated. "Anything else? I need to get going."

"No. There's nothing else." She turned away, vanishing in mid-step. John sighed, scrubbing a hand through his hair before going to find Rodney and begin powering the city down for the coming fight.


	8. The Siege pt 1

Author's note: RL really sucks. Sorry for the delay.

Things in this fic that don't belong to me include characters, plot, settings and most of the words.

The Siege 1

John hadn't been so grateful for Alice in a long time. This was the fourth...maybe sixth...briefing in the last two days, and he hadn't actually managed to sleep inbetween. Alice was keeping him awake, talking over Rodney where necessary when John's attention started drifting.

"Not only has Teyla been able to ascertain that the Wraith are more interested in Earth than Atlantis, which is, you know, terrifying, she realised that the hive ships will go right past the only surviving LaGrange point satellite."

"The last of what we assume were dozens of defence satellites destroyed during the Ancients' last stand with the Wraith," Zelenka clarified.

"That satellite's dead," Alice murmured.

"Yes, yes, yes..." Rodney waved Zelenka down. "The point is, we think we can use it to our advantage."

"I thought you said it was dead," John protested.

"It is, but we think we've learned enough about how it works to bring it back."

"If we are right about what is wrong with it," Zelenka muttered.

"Yes, of course if we're right about what's wrong with it! But if we're right, and it's just out of power, the Wraith have simply been ignoring it."

"Our preliminary estimates indicate a single naqahdah generator would be enough to bring it back online."

"Why can't we use our generators to get the weapons systems of Atlantis working?" Ford asked, interrupting what was fast becoming a squabble between the two scientists.

"Because those systems were designed to be powered by the Zero Point Module – and the satellite isn't."

"And you think it's powerful enough to take out a Wraith hive ship?"

"More than powerful enough," Alice said indignantly.

"According to the Ancient database, it should be able to take out all three when fully charged," Rodney told him. "Keep in mind that the Ancient technology was far superior – they only lost the war because they were vastly outnumbered."

"Well, we're vastly outnumbered!"

"And outgunned," Bates muttered.

"But they don't see the satellite as threat," Zelenka explained.

"In military parlance, surprise..." Rodney frowned. "Is an element on our side."

"What do you need?" Elizabeth asked.

"The satellite's fifteen hours away by Puddlejumper. I recommend that we put together a small crew – say myself, Grodin and a pilot."

"I'll go," John offered.

"No, Miller can handle it," Elizabeth said. "Major, I need you to keep searching for alternate Alpha sites, just in case this fails."

"The hive ships will be in range of the satellite in forty-nine hours. We're gonna need every last second of that time."

"Questions?" Elizabeth asked the room. "OK, let's get on it. Well, Rodney, I don't mean to put any undue pressure, but at this moment, that satellite is the only thing standing between the Wraith and Atlantis."

She left before he could answer: John clapped Rodney's shoulder, grinning. "No undue pressure."

"Pressure? Listen, after this year it takes a bit more than imminent death to worry me."

"Good, because this is a bit more than imminent death."

"Very funny."

"You think you can fix the satellite?"

"I think if I don't fix the satellite, we're all dead. Which also doesn't worry me. This was a bad year."

John's radio activated. _"Major Sheppard, please report to the infirmary."_

"on my way, Carson," he acknowledged.

"Hey, if he's handing out sedatives, I want one," Rodney said.

"What, and miss all the fun? Miller'll be ready when you are."

* * *

The corridor outside the infirmary was empty, and he slowed to a halt, fiddling with his radio. "Can the satellite be fixed, Alice?"

"I can't talk to the satellite from here. I don't know what's wrong with it. If it's just a loss of power then McKay is right, your generators would be enough for one battle. If it's something else..." She shrugged helplessly. "They're looking for you." She gestured to the infirmary door.

"Stick around," he told her. "I might need you later."

"I'm always around."

John didn't bother answering that, ducking into the infirmary. Carson was standing by Teyla's bed, arguing something with her, but both broke off when he appeared.

"Hey, guys." To Teyla, he added, "How're you feeling?"

"I am fine."

"I'm looking for something a little more enthusiastic than 'fine'." He glanced at Carson for help.

"I am ready to be put back on active duty," Teyla insisted.

"I'm sure you think so but, uh..."

"Tell him I am fine," she told Carson.

"She is, Major. I see no further reason she should be kept here under medical supervision."

Teyla looked back at John, who shrugged. "Alright. You're back on active duty."

Teyla sighed in relief, sliding off the bed as he turned to leave.

* * *

Alice was smiling when John passed her on his way to the briefing room; he slowed, raising an eyebrow, and she fell into step beside him.

"McKay and Zelenka are telling each other that they're friends, and not to get into trouble while he's away. But they're doing it by telling each other how stupid they are."

"Sounds like McKay," John said under his breath.

"It's happening all over the city. People are saying goodbye."

John slowed, wondering if he could get away with turning aside to talk to her, but Elizabeth was standing in the doorway of the conference room, watching him, and he sped back up. Bates was already inside, staring at his laptop, and John slid in beside him.

"M85-393?" Bates asked a while later.

John shook his head absently. "No. We've only been there at night and it gets ridiculously hot during the day, so no – not really an option."

"We wouldn't be having this problem if the damn Alpha site that we'd picked hadn't been marked by the Wraith," Elizabeth muttered.

"They're a real pain in the ass, aren't they?"

"Yes they are!" she agreed, smiling reluctantly.

"How about M4H-212?"

"No," Bates said. "Crawling with Genii spies."

"You know that for a fact, Sergeant, or is your spidey sense just tingling?"

Bates grinned, still studying his screen. "It's a fact, sir."

"Here we go," Elizabeth said suddenly. "M1M-316. Stackhouse reported lush surroundings, and as far as his team could tell, it seemed uninhabited."

"I'll get my team together and check it out," John agreed.

"OK, good. Remember, Major, we don't need ideal. I think we'd all settle for close."

"I'm on it."

Bates followed him out of the room. "Major. Is Teyla coming with you?"

"You're not seriously asking me that?"

"I think that's a bad call, sir."

"Here we go again!" He turned away, heading down the hall again; Bates stayed on his heels.

"All I'm saying is, we still don't fully understand her connection to the Wraith and, in my opinion, I don't think we should expose her to information we wouldn't want the Wraith to have – not the least of which is the location of our evac site."

"The doctor gave her a clean bill of health," John told him.

"And that's good to hear, sir, but if she can't control how the Wraith use her..."

"You don't know that," he interrupted.

"That's right, we don't! She saw everything they saw – who's to say they can't do the same with her, see what we see? If she's been compromised in any way..."

"She's an integral part of my team. Period. End of story. We're done here." He turned sharply away, leaving Bates behind.

"It's his job to think of those things," Alice reminded him. "You gave him that job."

"Suppose you don't trust her either?"

"I'm not..."

"Programmed for trust. You need new lines."

"I trust you. If you trust her, so do I."

"Nice to know."

"Besides, it's nice to have someone else talk to me every so often." She glanced away. "Your team's waiting for you."

"That was fast."

"They want to be doing something, I suppose." She turned away. "I'll watch the city for you, John."

"Thanks," he said, watching her leave. "Yeah, we definitely need to have a talk," he muttered, heading towards the ward room.

* * *

Seeing Bates glaring at Teyla was not what John needed after running for his life.

"I told you she was a liability, sir! Now I'm not gonna let your personal feelings endanger this facility any longer!"

"What?" Teyla asked in surprise.

"Look, I'm not accusing you of doing it intentionally, but the Wraith must be getting information from you!"

"What the hell are you talking about?" John demanded. "We ran into a...uh... what the hell was that?"

"Looked an awful lot like a T-rex, sir," Ford offered. He was standing squarely beside John, backing him up.

"Yeah, a T-rex. It wasn't even a Wraith! So why don't you check those accusations?"

Elizabeth finally managed to break in. "I take it you don't recommend the planet as an Alpha site, Major?"

"Wouldn't be my first choice. If McKay doesn't get the satellite online, we're screwed."

Bates backed off, still muttering angrily, and John brushed past him, passing his weapon off to the nearest soldier. Bates turned on his heel, heading away.

Teyla stood for a moment before following him. Ford tried to stop her, but she brushed past him without even stopping and he gave up, heading away.

"Sergeant Bates!"

Bates paused, looking back at her. "What is it?"

"You just accused me of disclosing our position to the Wraith."

"Yes, I did."

"Clearly you were wrong."

"That's yet to be determined, ma'am."

Teyla took a deep breath, reminding herself firmly that John would not be happy if she attacked him. "Excuse me?"

"Look, I'm willing to accept that you're not fully in control of what information you give away, but it's still my opinion that you should not be allowed to move freely around this base of operations."

"Perhaps you are not aware, Sergeant, but being accused of serving the Wraith is the greatest insult among my people."

"Oh, I'm aware," Bates said smoothly.

Teyla elbowed him in the face.

John grabbed her from behind, yanking her bodily away; Ford slid between them, blocking Bates when he went to retaliate.

"I was simply stating an opinion, Major!" Teyla spat, twisting against him.

"She attacked me!" Bates protested.

"And for good reason!"

John pulled Teyla away again. "Yeah, what reason would that be?"

"My guess would be the Wraith!"

Teyla almost got past John at that; he jerked her back. Bates almost knocked Ford over as he struggled.

"Walk away, Bates," John ordered.

"Sir..."

"Walk away!"

Bates pulled free of Ford, pointing angrily at Teyla. "This isn't over."

"I would be disappointed if it were!" she yelled after him.

John waited long enough to be sure he was really gone before rounding on Teyla. "What the hell are you doing? You don't go around decking the head of security!"

"He said..."

"I don't care what he said!" he interrupted. "He _says_ a lot of things. You just stay away from him."

Teyla glared before turning away. Ford whistled as she disappeared around the nearest corner.

"You saw nothing," John told him.

"Aye sir," Ford agreed, heading away.

Alice watched, frowning. "Teyla doesn't normally hit people."

"Hey," John protested.

"Unless she's teaching you to fight," Alice corrected herself.

"Better." He frowned down the corridor. "That happening all over as well?"

"Some. No one else is accusing anyone of helping the Wraith, though."

"No one else is stupid enough to believe it," John muttered. "Keep an eye on it for me, ok? Let me know if anyone else starts getting serious." She looked away, biting her lip, and he demanded, "What?"

"You need to lift the restriction on my entering your quarters if you want to be told of anything that happens."

"I already lifted that."

"For the Wraith arrival."

"You..." he cut himself off, rubbing at the bridge of his nose. "All right. For the duration, use your judgment and come tell me anything you think I need to know. All right?"

"Yes. Thank you. You should talk to Zelenka."

"Zel...why?"

"He's trying to find a way to clear the database. I can do that, I've already said I would. It's time he could be spending on other things."

"Why is he trying to delete you?"

"To save it from the Wraith. Elizabeth told him to."

"Well, then let him do it. Never hurts to have backups." He studied her for a moment. "You're coming with us, you know."

"No?" She frowned. "I'm Atlantis, John."

"We'll be taking the 'Jumpers."

"The Gate ship program is only a fraction of this version of me. You know that."

"Still you," he said quietly. "We're not leaving you behind."

She hesitated before smiling. "No. I know."

John nodded, turning away again. "Thanks for calling me," he said over his shoulder. He glanced back when she didn't answer, but she'd already vanished.

* * *

John was seriously starting to consider moving his cot into the Conference room. He'd get much more use out of it.

"What about M1K-439?" he suggested.

"Which one's that?" Ford asked.

"The one with all the waterfalls."

"The waterfalls...see, now, why don't we just call it Planet Waterfall?" Catching John's look, he added defensively, "What? I say we should just give 'em names! Look, we've got a list of five planets here. That should be enough potential Alpha sites to get Stackhouse and his team started."

The voice on the tannoy surprised them both. "_Major Sheppard. We have a situation at Generator Station One_."

John frowned, glancing automatically around. Alice wasn't there, and he gestured for Ford to follow him.

* * *

A Marine was crouching over Bates when they reached the generator station. "What's the problem?" John demanded.

"It's Bates, sir."

"What about him?"

"He's been attacked."

John grimaced, looking down at Bates. Someone had really gone to town; the sergeant was bruised and bloodied.

"Get a medical team down here," he ordered, moving out into the corridor. As soon as he was out of range of the lab he hissed, "Alice?"

"Yes, John," Alice said from behind him.

"What the hell happened in there?" he demanded.

She looked past him, blinking. "I'm sorry, John, sensors are down in this area."

"Sensors are...since when?"

"It's temporary. A maintenance issue. What's happened?"

"Bates has been attacked!"

"Oh." She looked away. "I'm sorry. No sensors picked up anything suspicious."

"You're sure? Check everything."

"A complete check of the sensors will take time, John."

"Do it anyway. What's up with you? You're all...formal."

"I'm currently active in several locations around the city. It slows processing."

"Where are you active?"

"Teyla's quarters, Elizabeth's office, Zelenka's workspace and three other labs, the Mess hall, the Infirmary, the..."

"Ok, point taken. Just...see if you can find out anything, all right?"

"Yes, John."

* * *

It was early the next morning, just after dawn, before Carson was able to give them a report. John and Ford had been waiting in the infirmary since Bates had arrived.

"Is he gonna be OK?" John asked when Carson joined them.

"It's still hard to tell. He's got five broken ribs, a fractured collarbone, and the concussion was quite severe."

"When can we talk to him?"

"We can't. I put him in a medically induced coma until the subdural haematoma can be dealt with. We won't be finding out what happened from him any time soon."

Ford shifted uncomfortably. "Teyla and Bates got into it pretty badly yesterday, sir."

"A fistfight and a beating like this are a long drive apart, Ford."

"I understand that, sir, but they were in a fight; they were both looking to continue it."

John grimaced, looking at Carson. "Anything pointing to who did this?"

He shook his head. "I'm having a forensic exam of both his body and clothing performed right now."

"Let us know what you find out." To Ford, he added, "Let's go get her side of the story."

* * *

Teyla hadn't been sleeping, apparently, so John felt a little better about bursting in on her with Ford in tow. And even if she had been sleeping, she woke right up once she heard why they were there.

"You do not think I had anything to do with it?" she asked, looking from him to Ford and back.

"Of course not," John said quickly.

"You and Bates did get into it pretty good yesterday," Ford said neutrally.

"You _know_ me, Aiden. I never would have taken it that far."

"I know," Ford agreed, "so let's just see if we can't rule it out altogether. Where were you last night?"

"I was here, in my room."

"The whole night?"

"Yes."

"So there's no way of knowing whether you blacked out or not?" John deliberately raised his voice, trying to provoke Alice into appearing, but there was no sign of her.

"I have no way of proving it, no, but I did not leave this room last night – I am sure of it. I did not leave this room." Teyla was watching him warily; he nodded quick confirmation, ignoring the doubt on Ford's face and turning to leave.

* * *

"Alice!" he hissed later.

She appeared in front of him, looking past him for a moment before she refocused. "Yes, John."

"Where was Teyla last night?"

"In her room. Talking to me, on and off. Why?"

"Talking to you?"

"She's the only other person who knows about me. Sometimes she thinks out loud."

"And how do you join in?"

"I listen. What else can I do? Why do you need to know where she was?"

"Because Bates was attacked," he reminded her, "and we don't know who it was."

"It wasn't Teyla." She studied him for a moment. "Did you think it was?"

"No. I didn't. You still..." He gestured vaguely. "Processing slowly?"

"I'm still active in multiple locations, yes."

"How come the Ancients didn't plan on that? What good is a program that slows down the more it's used?"

"They did plan for it. I'm supposed to run on the ZPM, remember? I use three of your generators just to keep going."

"Be careful, then."

"I will, John."

"I gotta go report to Elizabeth. Come with me."

"I'll meet you there," she promised, vanishing.

* * *

It took him longer than he'd thought to round up Ford; night was falling as they reached Elizabeth's office. She'd been keeping up to date and knew that Teyla was currently their top suspect, although she didn't like it any better than John.

"I know there's no love lost between her and Bates, but I can't see her beating the hell out of the guy," John said, finishing his report.

"Also, you know it wasn't her," Alice muttered.

"Ford?" Elizabeth asked.

"Ma'am?"

"What do you think?" she pressed.

Ford glanced uncomfortably at John. "I worry about what she might have done unknowingly. The whole Wraith connection thing and her nightmares make me nervous."

"Yeah, well, what are we gonna do about it? Stick her in the Brig? This is _Teyla_ we're talking about."

Carson leaned into the room. "We have a situation on our hands."

"What's going on?" Elizabeth asked, rising to her feet.

"I've completed the tests. I found DNA on Sergeant Bates' uniform."

"And it's not Teyla's?" John asked quickly.

"No, Major."

"Who is it?" Elizabeth asked.

"I ran the tests twice to be certain. It's conclusive. We have a Wraith in the city."

* * *

John excused himself on the pretext of informing Teyla himself; the corridors were crowded, and he didn't stop until he reached her quarters.

Teyla let him in without question; Alice was sitting cross legged on the edge of the bed, watching as he paced.

"It wasn't you," he said, and Teyla smiled wryly.

"Thank you, but I believe we had established that. Who was it?"

John looked over at Alice. "Anything you want to tell me?" She shrugged, palms up, and he added, "About a Wraith in the city?"

"There are no Wraith here," Alice said in surprise. Teyla had risen to her feet, but she didn't attempt to interrupt.

"Bates was attacked by a Wraith. Carson's proved it."

"There are no Wraith here! That's a primary function! If there were Wraith, I would..." She cut herself off, looking away.

"What?" John asked. "What?"

"Sensors. The sensor malfunction..."

"Not a malfunction," he finished. "Can you see him now?"

"No. But there are sensors out in several of the lower levels. I can't...nothing down there is registering."

Turning to Teyla, John said, "It was a Wraith, but we don't know where it is."

"I gathered that," she agreed.

"The others are waiting in the conference room. Let's go." To Alice, he added, "You too."

"I'll meet..."

"No," he interrupted her. "Stay with us, this time."

"All right," she agreed, frowning, but she was on his heels when he left.

* * *

Elizabeth was already in the conference room with Ford, Carson and Zelenka; John hesitated in the door, watching Ford murmur an apology to Teyla, who smiled at him.

"John, you're standing in the door," Alice said from behind him.

"Like it bothers you," he muttered, coming forward to join the group. "Someone tell me how this is possible. How can the Wraith get inside the city?"

"They didn't gate in," Ford said.

Zelenka lifted his head. "The Dart."

"What?"

"The Wraith Dart that scanned us. It made its way through the city, scanning for data. The second it was done, it self destructed."

"So it beamed into the city," John said slowly.

"Can they do that?" Ford asked.

"The same technology that is used to sweep people up and into their ships must work in the opposite way," Teyla guessed.

"So the pilot of the Wraith Dart scanned us, transmitted his information to the hive ships, beamed down here and destroyed his ship." Elizabeth glanced around at them.

"Yes, yes. It seems possible."

"That is precisely the time I started to sense the Wraith continually," Teyla said slowly.

"No wonder you were having nightmares," John muttered.

"What's he been doing here all this time?" Elizabeth asked.

"Well, Sergeant Bates was attacked near the naqahdah generator that powers this tower," Zelenka offered.

"The Wraith must have been doing recon. Maybe his job is to knock out the power before the hive ship gets here – leave us dead in the water."

"Or to make sure any self destruct plan we had in place wouldn't work," Ford added.

"Maybe a combination of both," Elizabeth suggested.

"Exactly."

"What we do know for sure is that we have a Wraith intruder in the city that we have to track down."

Zelenka raised a hand. "I have an idea."

He slid past John into the control room; the others followed, and John waited long enough to ask, "What's he doing?"

"I don't know," Alice said with a frown. "That isn't...oh, the life signs reader. Good plan," she added, impressed.

"Life signs..."

John cut himself off, reflecting sourly that he seemed to do that a lot around her. Outside, Zelenka was speaking, and he joined the group in time to hear "...online for past month or so. It detects irregularities in biometric rhythm and reports them."

"Wouldn't it have picked up on the Wraith?" he asked.

"Well, it requires significant amount of power, so we've narrowed its field of focus to scan solely in the Gateroom, figuring that was the only place that the Wraith ... or any other alien, for that matter, would likely enter the city from."

"OK, so that was wrong." He glared at Alice, who glared right back at him.

"I can't change where it looks," she reminded him. "And I can't see anything that isn't on the sensors."

Zelenka had mostly ignored him, fiddling with the controls. "Now, if I could only expand the scanning field to ... My God!"

"What?" John demanded.

"That's him – look."

Either Zelenka or Alice zoomed the map in, showing a red dot.

"It works very much like the lifesigns detector, but it's able to distinguish different lifeforms," Carson said.

"That's him?" John asked.

"That's him," Zelenka agreed.

"You can track him in real time?"

"Yes."

John turned, gesturing. "Ford, Teyla: we need two teams. Let's go get him."

"Yes, sir," Ford agreed, following him out with Teyla.

* * *

John sent Ford and Teyla off together and took a couple of the Marines to make up his own team. The Wraith hadn't moved since they'd started, but Zelenka was glued to the display in the Control Room.

"Is he still in place, Doc?" John asked his radio.

_"Yes. He's still in the same room. Hasn't moved since we located him."_

"Let's hope he's still sleeping. Ford, Teyla: you in position?"

"_Almost,_" Teyla told him.

"My team's ready. We're gonna breach the room at the same time from different directions. If he tries to get out the other door, take him."

"_Understood, sir,"_ Ford said._ "We shouldn't be more than a couple of minutes."_

"Alright. Stand by." He motioned his team into place.

"John," Alice said suddenly, taking two quick steps back out of his line of sight. The door hissed open; when nothing happened, the Marines edged forward.

A wave of energy burst from the room, knocking them all back. John gasped as he thumped into the ground; he was vaguely aware that the Wraith had appeared, but his muscles weren't getting the urgent messages from his brain.

The Wraith crouched beside him, knife in one hand. "Nothing will keep us from our new feeding ground," it said softly, raising the blade.

John tensed, unable to do any more than that, but a stunner blast hit the Wraith from behind and it collapsed, blade falling from limp fingers.

"You were on vox, sir," Ford explained, crouching beside the Wraith and examining it. "We heard the whole thing and double-timed it."

Teyla crouched by John, who blinked as best he could. "We got it, Major. You're going to be OK."

* * *

Alice was sitting cross-legged on the end of his bed when he woke up in the infirmary. Carson was audible somewhere nearby, but the curtains were pulled closed.

"That may have been the most rest I've had in a while," he said idly, squinting at the ceiling.

"You were stunned, not sleeping. I'm not sure it counts as rest."

"How's the city?"

"Much the same. Your Wraith is in the brig. Are you planning on keeping him?"

"Haven't decided yet."

Carson pulled the curtain aside, eyeing him. "Still talking to yourself, Major?"

"Got to do something to keep myself occupied. Can I go now?"

"Give me a minute to check you out, Major," Carson protested. "How're you feeling?"

"Just pins and needles. I'm fine. I really have to go, though."

"Aye, you'll be wanting to go see your Wraith, I suppose. All right, go ahead. But you'll come back..."

"...if I feel anything else, yes. I will."

* * *

Alice caught up with him again in the corridor outside the infirmary. "Ford's in the brig, with the Wraith," she said, anticipating him. "John, I'm not going in there with you."

"Why not?" he asked absently, stepping into the nearest transporter.

"Because I was programmed to help fight the Wraith, not hold them. The only reason alarms aren't going off all over the city is that I'm suppressing them...Wraith never, ever set foot here. That's also a primary directive."

He considered her for a moment, nodding. "All right. I'll see you later, then."

She'd vanished by the time the door opened, and he headed down to the brig, picking up Teyla on the way.

Ford was watching several other Marines watch the Wraith. "Good to see you on your feet, sir. How're you feelin'?"

"You know, pins and needles." John shrugged. "Hate getting stunned by those damn things. Has he said anything yet?"

"No sir, not yet."

"You got a name?" John asked. The Wraith eyed him but didn't answer. "OK – we'll go with...Bob. Bob – I'm gonna need to know what you've been doing here for the past two weeks, and I'm gonna need to know now."

Bob still didn't answer, sneering at a point somewhere in front of him. John took a step back, turning to Ford and Teyla.

"I don't think he's in a very talkative mood, sir," Ford offered.

"Yeah," John muttered. "I need to know what he's been doing and whether or not he's been transmitting back to the hive ships."

"Wouldn't we have picked up a transmission?" Ford asked.

"We can send secure messages – there's no reason he can't."

"Maybe I can try and connect with him," Teyla offered.

John shook his head. "I don't think so."

"If the Alpha site has been compromised, Major, we need to know," she pointed out.

John looked back at the Wraith for a moment, turning back to her. "OK, see what you can do."

Teyla crossed to stand in front of the cell, watching the Wraith carefully. John watched her as she took a deep breath before locking her gaze on Bob.

"What are you doing, human? You're trying to get inside my mind. Allow me."

Teyla stumbled, grasping at her head and collapsing.

"Teyla?" John yelled. "Stop it! Shut it off!"

Ford dropped beside Teyla, prying her hands away from her head. One of the Marines turned off the forcefield and John shot the Wraith, twice. It growled, more or less unhurt, but the distraction worked and Teyla sat up with a gasp.

"Are you OK?" Ford asked. Teyla nodded, gripping his arm.

"My wounds will heal," Bob told John.

"Yeah, but for how long?" He shot it again...and again. Five times in all. Bob collapsed to his knees, snarling. "I need to know what you've done to this city. Listen, Bob, I have no problem with killing you whatsoever."

He shot twice more, ejecting the clip and loading a fresh one.

"I'm not screwin' around, Bob! Did you sabotage this base or not?" He fired another three times, finally overwhelming Bob.

"Those who feed upon you will know what you've done to me," he warned John.

"Yeah. We'll see."

"Sir," Ford said quietly. "I think maybe we've gone a bit too far."

"I don't think we've gone far enough."

"John," Alice said quietly from the door. He turned, stalking into the nearest corner. "McKay has been in contact. They destroyed one ship, but the satellite's gone. Peter Grodin was on board at the time."

"Damn," he muttered, rubbing his forehead. "What about the other ships?"

"They've stopped for now. McKay's on his way back."

John started to answer, but paused when the tannoy whistled. "_May I have your attention, please? This is Doctor Weir. Our plan to stop the Wraith armada has failed. They will make it to Atlantis. Therefore we must begin our evacuation plans. I wish I could tell you all that this is a fight that we will win, but I can't do that. I wish I could tell you that we will find a safe harbor when we leave here. I can't promise you that either. I can tell you this: up to now, you all have accomplished extraordinary things, and I believe that even in the face of an uncertain future, as long as we stay together we have a chance to continue to do so. Now, we all have our evacuation duties, so thank you – and I'll see you on the other side."_

Alice closed her eyes. "Zelenka's virus program is ready to go."

Bob propped himself up on one elbow, glaring at John. "I will tell you this: no matter where you flee, we will find you – just as surely as we will find Earth. And when we do, we will feast."

John calmly emptied the rest of his clip into it, watching it die.

_To be continued._

_Trecebo: Thanks. I like to think so._

_Duchess: Yeah, I'm Irish, so I tend to use English spellings._

_Eris: Thanks! I figure she's got some of that Ancient cockiness. :) Second season coming soon._

_Study in Scarlet: Thanks! Looking forward to hearing from you again._


	9. The Siege pt 2

Author's note: Siege pt 2. Enjoy! Second season's on it's way.

The Siege 2

John was surprised Elizabeth hadn't yelled at him. She knew about the Wraith, but she hadn't mentioned it to him yet, either to blame or thank.

He trailed her into the control room as Rodney came down from the Jumper bay above. "Welcome back, Rodney."

"Where are we?" he asked, automatically moving to the scanner console.

"Our scanners show the hive ships have started moving again, although their pace has slowed considerably." Elizabeth joined him, eyeing the path of the ships.

"Obviously you gave them something to think about," John offered.

"If they get here in two hours or two days, doesn't change the fact that we're out of options. We can't hope to fight them. So unless either of you have any more ideas. . ." Elizabeth glanced from John to Rodney and back.

Ford came in, glancing from Elizabeth and Rodney to John. "The last group is assembled and ready for evac."

"All right then," Elizabeth said. "Let's get this done." She turned to her laptop; John went to another one.

"Ready?"

John nodded, setting the self-destruct. Elizabeth matched it on her end, flinching despite herself when the alarm started blaring.

"Self-destruct is armed. Prepare to load the virus into the Ancient mainframe. Rodney, dial the alpha site."

"Dialing."

Alice drifted towards his console, watching as he dialed. "Incoming," she murmured, a second before the 'Gate activated.

"We've got an incoming wormhole," Rodney said in surprise. "Receiving IDC."

"Who is it?" John asked.

"Stargate Command," he said disbelievingly.

"Are you sure?"

"Confirmed," Alice told him as McKay said, "Positive!"

"Lower the shield," Elizabeth said, turning to the rail. Rodney lowered the shield and followed John towards the 'Gate room.

Ford was already there, watching as a group of Marines came through, carrying boxes. Most of them ignored him; he saluted the leader, getting a nod in response.

"Doctor Weir?" he asked.

"Yes."

"Colonel Dillon Everett, United States Marine Corps."

"You should know that we—"

"General O'Neill sends his compliments on a job well done under extraordinary circumstances," he interrupted, saluting without enthusiasm. "You are relieved."

"Sir, we're about to evacuate," John protested.

"Without a fight," Everett clarified.

John hesitated, glancing at Elizabeth. "Yes, sir."

"On my order," Elizabeth added.

"That evacuation order is rescinded. I assume you've armed the self-destruct device?"

"Yes, we have, but as Doctor Weir was trying to tell you-"

"I am going to need you to disarm it immediately."

Elizabeth shook her head, fed up. "Hold on a second, Colonel. I don't think you fully grasp our situation here."

"You have three Wraith hive ships bearing down on your position and precious little to defend yourselves with," Everett said over-patiently. "That about sum it up?"

"You got our message," Rodney realized.

"We got your message," he agreed.

"It's down to two hive ships," Elizabeth told him. "We managed to destroy one."

"Good for you! That should make my job a little easier."

"What exactly is your job, sir?" John asked.

"I should think that would be obvious to you by now, Major. We are going to defend Atlantis at all costs."

"I don't think I like him," Alice muttered. "John, if we're going to fight now maybe you could turn off the self-destruct? I'd rather not blow up or be erased."

He waved her to silence, watching as Everett passed his orders to Elizabeth. "Signed by General O'Neill."

Elizabeth scanned the sheet. John read the first couple of lines over her shoulder, enough to know it was legit.

"Colonel, it's not that we don't appreciate the thought," he said carefully. "But if you had read the report on the armada that's headed this way, you'd know that there's not much we can do about it."

"Oh, I've read your report cover to cover, Major."

"He really doesn't like you, does he?" Alice asked.

"Must have found a Zed-PM," Rodney was saying. "That's the only way they could have dialed in from Earth."

"It was discovered in Egypt by a group of archaeologists," Everett told him. "Damn thing's been under our noses the whole time."

"Fantastic! Wa- Wait a minute. How can you possibly bring the Zed-PM back here? I mean, you need it to maintain the wormhole."

"As we speak, it is being transported up to the Daedalus, our new battle cruiser."

"Oh, sister ship to the Prometheus. I didn't even know it was finished."

"You have battle ships? Why aren't there any of those here?" Alice asked, frowning. John rolled his eyes at her, trying to look as though he was listening to Everett.

"With a ZPM boosting her engine, she should be here inside of four days. That is how long we have to hold this base. Major Sheppard, dial Pegasus alpha site, recall all military personnel; as well, any civilians who'd like to return and help take part in damage control are welcome to do so." He started towards the steps; John rolled his eyes to Alice again and followed him. "And when you're done with that, please join me in my offices and conference room. We'll discuss our tactical position."

"Colonel Everett!" Elizabeth called from below. "Fine, you're in charge. But I should be at that briefing."

"When it comes down to any other aspect of Atlantis, I will be happy to include you. We're talking about our tactical position."

"I understand that-"

"Good! Somebody want to please turn off that self-destruct!"

John lingered for a moment, looking helplessly down at Elizabeth. She waved him away resignedly and he followed Everett towards the conference room, pausing just outside. "Alice? Any of his men have the gene?"

"No. Still just you."

"Stick around."

"Always do."

Elizabeth caught up to him. "We need to turn off the self-destruct, Major."

"Good, I was about to do it myself," Alice muttered. John raised an eyebrow at her and she added, "No, I can't really do that. But I can annoy you until you do."

He grimaced at her, turning to the nearest laptop to enter his codes. The alarm shut off and he glanced at Elizabeth. "I need to call the Alpha Site."

"Not yet. I want to talk to him first."

"Elizabeth..."

"Just let me talk to him, John."

* * *

Everett was studying a schematic of the city when they came in: John ignored the faintly disapproving look, falling into a loose at-ease stance. "Self-destruct has been aborted."

"Thank you. Did you contact the alpha site?"

John glanced at Elizabeth, who answered on his behalf. "I asked Major Sheppard to wait until I had a chance to talk with you."

"Is that a fact."

"Yes, sir," John said.

"Major, dial the alpha site."

Elizabeth halted him. "Colonel, you've been here all of five minutes. Now, I have been responsible for the lives of the people on this base, both military and civilian, for the past several months. I'm not about to put those lives in jeopardy until I at least know how you intend to defend this city."

"I don't need to explain myself to you, Doctor, and I don't need your cooperation."

"But you could probably use mine," John said easily. "Sir. So with all due respect, please answer Doctor Weir's question."

"Is that a threat, Major?"

"Careful, John," Alice warned him. "He's only looking for a reason to get rid of you."

"No, sir," John said, slightly more politely. "I understand you need to establish a clear chain of command. But if you cut Doctor Weir out of the loop, you'll only alienate the people whose trust and respect she's earned, which is everyone on the base. Including me."

"Is that a fact." He took a moment to study them. "Have a seat."

Alice trailed John, standing beside him when he sat. "This is not a nice man," she muttered.

"Six naquadah-enhanced nuclear warheads, twelve hundred megatons apiece," Everett began. "They emit almost zero EM and are otherwise invisible to radar. Once deployed, they will detonate by proximity fuse."

"Space mines?" Ford guessed.

"That's right. We use jumpers in stealth mode to place them in a pattern between the armada and Atlantis. Major, we were hoping you could help us with that."

"Yes, but I recommend keeping a couple in reserve."

"Negative," Everett said. "We're only going to get one shot at this."

"We have to consider the possibility-"

"Four of my men are pilots," Everett interrupted him again. "Beckett is giving them the gene innoculation right now. Assuming it takes, you will familiarize them with the jumpers, and they will become our fighter screen."

"Along with me," he agreed.

"I have another job for you. I understand that this base is equipped with a chair weapons platform like the one we found in Antarctica."

"Yes, but we have no way of powering it," Elizabeth said.

"We do now. We brought a Mark II naquadah generator."

"We found a way to increase the power output by six hundred percent," one of his Marines explained. "It won't last nearly as long, but should be able to power the chair for as long as we need it to."

"This is beginning to sound like a plan."

"I'm glad you approve. We know this is a long shot, but like I said, all we have to do is hold out until the Daedalus gets here. Then we can use the ZPM to power the city shield. Any questions? All right then. Now that Doctor Weir has been informed of our plans, I would greatly appreciate it if you'd execute my order and contact the alpha site."

"Yes, sir," John agreed, rising to his feet.

"And Major?" Everett added. "This is the last time I give you an order twice."

"Understood."

* * *

Until the gene took in Everett's pilots John had very little to do; he walked the City, watching as the guns were installed, armed and tested, and as work began on the chair.

"You don't like Everett much, do you," he murmured.

"He doesn't like me. He doesn't see the City, just a base. Something useful to him."

"He hasn't had much time yet."

"Time won't make a difference. Not to that one."

"He's still my commander, Alice."

"Yes. You have to follow his orders. I will follow yours."

John nodded, sighing. "His pilots'll be ready by now."

"Yes," she agreed. "They are on line." Off his look, she added, "The artificial gene is never as strong as the real one. You're still the only one to see me."

"Good," he muttered, turning away and heading for the nearest transporter.

* * *

"Can you talk to the other 'Jumpers?" he asked later, leading the fleet out of the city.

"Well enough. Less as we spread out. Why?"

"Because the first time any of them saw a 'Jumper was half an hour ago. I want to know if they're having problems."

Alice nodded, eyeing his HUD. "Will this plan work?"

"Should do. The mines are strong enough..."

"Three's drifting."

John tapped his communicator. "Jumper Three! You're drifting out of line."

_"Sorry, sir_," the Marine called. His 'Jumper slid back into line.

"Better. Watch your HUD." He clicked the communicator back off. "The mines are strong enough to hurt the ships, at least."

"As long as they don't deviate from their course," Alice pointed out. "You have only enough to cover this approach."

"The Wraith want the City. This is the way they'll be coming." Flicking on his communicator again, he said, "All right, we're nearing drop point. Everyone spread out."

* * *

They were almost back to the City when Alice said conversationally, "The Chair's running."

"Good," John said absently.

"But there are almost no drones. Less than four dozen."

"How did that happen?"

"They were used in the war. When the People knew they were leaving, they stopped replacing them." She glanced away. "Sensors are picking up something else...John, get to Control. Fast."

The alarm was blaring when the 'Jumper landed; John left the pilots behind, running for the control room.

"What's going on?" he demanded, skidding to a halt beside Rodney.

"We just detected a wave of - objects approaching the planet," Elizabeth told him.

"How many?" Everett demanded.

"Hundred plus," one of the techs told him.

"How come they weren't detected by the long-range sensors?" John asked, watching Alice boost herself up to sit on the console.

"Because they're rocks," Rodney said absently. "Asteroids. The Wraith must have harvested them from the system's asteroid belt and accelerated them towards us from a safe distance. The mainframe's taken this long to determine that they were a threat."

"Can they do much damage?" Elizabeth asked.

"Oh yeah. Even if most of them burn up in the atmosphere, but that's not why they're doing it."

"They're headed toward the mines," Everett realized.

"Well, can they be deactivated?" John asked.

"No."

"That was smart," Alice murmured, leaning over precariously to watch the screen. The asteroids careened into the mines; the screen blanked out and Alice frowned, shaking her head. "John, my long range sensors are all down."

"Well. That's that." Rodney pushed away from the screen, eyeing Everett. "Your mines make one hell of a bang, Colonel; I'm sure the Wraith's ears are ringing."

"What's the status of the hive ships?" John demanded.

"Sensors are down," Alice reminded him, overlapping with Rodney's, "There's no way of knowing. The mine detonation must have overloaded the sensors."

"How long till they're back up?" Everett asked.

"There's a lot of residual radiation," the tech pointed out.

"It'll keep us blind for hours," Rodney said bluntly.

"Yeah, well, they're still out there." John glanced at Everett. "We just lost our primary line of defense." Glancing at Elizabeth, he added, "I have to go debrief the pilots."

"Go ahead," she agreed. "Just don't take too long."

John stomped deliberately up the metal staircase, making enough noise to cover his words. "You ok?"

"I'm a little off balance," Alice admitted. "It's odd having so few sensors working."

"We didn't even know we had those sensors until a few weeks ago."

"They were still running, though. Powered up with the others. Go talk to your pilots, I'll let you know if anything changes."

* * *

The debriefing didn't take long, and John was on his way to find Rodney when Everett called him. Sighing, he headed for the hologram chamber instead.

Everett was staring upwards, though the hologram wasn't switched on. John stepped inside, pausing near the door. "You wanted to see me, Colonel?"

"I was told I could learn a lot about the history of Atlantis in this room."

John nodded. "We haven't used it much because of the power requirements."

"Still, I would like to see for myself how the Ancients lost the first time, try to avoid their mistakes."

"Yes, sir, we could do that." He stepped up to the control panel, starting the program.

"I'll do it," Alice said quietly. "Just keep talking."

John nodded absently, watching the map of the galaxy appear overhead. "This is the status of the Pegasus galaxy, before the Ancients encountered the Wraith. The blue stars represent systems either inhabited by or protected by the Ancients." He glanced at Alice and most of the map tinged red. "Then, this is how it looked after they fought for almost a hundred years."

"Until Atlantis was all that was left," Everett mused.

"Yes, sir. That's when the siege began." The display switched to the solar system; Lantea was directly in front of them. "For several more years, the Atlanteans were able to hold off their attackers, relying on the city shield and superior weaponry, including the weapon satellite system." Wraith ships began to attack the planet; he slanted a glance at Alice, who was watching without emotion. "No matter how many Wraith ships they destroyed, more kept coming. They could win almost every battle, but they saw no way to win the war. So, they submerged the city, and left."

The hologram shut off and the lights came back up. Alice was standing by the door, hands clasped loosely in front of her. "That's it, that's the story," he added. "But the picture is pretty clear."

"So you think this is a no-win situation."

"No, sir. What I mean is even if we beat them this time, they're going to come back."

"Major, I think I should tell you that Colonel Marshall Sumner was a very good friend of mine. We served together a lot of years, and you know, I cannot for the life of me figure how it is that you could go as far as you did and not save him, how you could get that close-"

"By the time I reached Colonel Sumner-"

"Worse, you admit to firing the shot that killed him!"

John took a deep breath. "Because I believed that's what he wanted me to do."

Everett took a step forward, into John's space. "You knew him that well, did you?"

"You weren't there, sir," John gritted.

"No. I wish for his sake I was."

"He's trying to provoke you," Alice reminded him. "He wants you off the team, out of the City, away from him. Don't let him have it."

John carefully took a step back, away from Everett. "There isn't a night that goes by where that moment doesn't play in my head. And every time it does-"

The alarm rang before he could continue, and he reached automatically for his radio, Everett mirroring him. "Control room," he said, perfectly echoing Everett. Grimacing, he took another step back, gesturing to Everett to go ahead.

"This is Colonel Everett. Report."

"_Sir, we've just detected a wave of Darts, inbound._"

"I'm on my way." To John, he added, "Get to the Chair. We'll finish this later."

* * *

"There are several signals," Alice said. She wasn't running—her legs weren't moving—but she was keeping pace with him anyway. "Everett's teams are ready. The City's gone dark all over."

John skidded into the Chair room. "McKay, fire it up!

"It'll take a minute."

"We don't _have_ a minute."

Rodney stopped what he was doing to glare. "Look, this generator can only power the Chair because it operates in a state of barely controlled overload."

"Just get the damn thing working."

"That's what I'm trying to do!"

The room darkened and Alice flinched, backing away from the Chair. John caught her eye and she said shakily, "Primary systems are off-line. The Darts are making suicide runs." Looking away, she added, "People are being taken."

Rodney straightened. "Okay, you've got power, go!"

John leaned back, eyes locked on something overhead.

* * *

For a long time all he could focus on was the Darts and the drones; with so few drones left he didn't dare to waste them, concentrating fiercely to make sure each one hit a target. Dawn was breaking by the time he ran out of things to shoot, letting the Chair power down with a sigh. His head ached, pounding in time with his heartbeat.

Alice was standing against the wall and he squinted, trying to figure out if she was really as pale as she looked or if the still too-low lighting was washing the color. "The City's burning," she said dully.

"You all right?" he demanded.

Rodney looked up from his laptop, frowning. "Yes, of course. I mean, I haven't slept in about twenty hours, and I haven't eaten in just as long, but other than that..."

Alice nodded without answering, and John made a face at her. "Where's Dr Weir?"

"In Control." McKay shut his laptop. "What about you? Any problems with the generator?"

"No. It's fine. Come on."

Rodney made a face, following him. Zelenka trailed after them.

* * *

John paused at the window near Control, staring at the City. The fires were mostly out, but smoke was still rising from several places and almost every building he could see was damaged in one way or another.

"God," McKay breathed from beside him.

"It's not as bad as it looks," John said absently, one eye on Alice.

"It's not," she agreed. "A lot of mess. Little structural damage." Turning away, she added, "Everett's looking for you."

John nodded, turning away from the window and heading for Control.

* * *

Everett and Elizabeth were leaning over a laptop, watching the status reports come in. John leaned against one of the consoles, watching Rodney bully them out of the way.

"Power's out in sections of the city," he told them. "The long-range scanners and the internal sensors are down, but we're working on it."

"I want to know the status of those hive ships ASAP," Everett said.

Rodney didn't look up. "They're coming! That's their status! Tomorrow, the day after, the day after that, eventually they'll get here! Whether we're here to greet them or not is another matter."

"Rodney..." Elizabeth murmured.

Rodney shook his head. "Look, the chair is out of drones. How do you expect to handle the next wave?"

Everett blinked. "I'm open to suggestions."

"Really."

"We target the hive ships," John said.

"With what?" Everett protested.

"We fly the puddle jumper in stealth mode right down their throats."

"John," Alice protested.

"Are you volunteering for a suicide mission?" Everett asked, eyeing him.

"Well, it won't _be_ a suicide mission if McKay and Zelenka can figure out a way to remote control the jumpers."

Everett glanced at Rodney. "Can you do it?"

"I _knew_ this was going to happen," Rodney said.

"Is that a fact."

"Yes, it's a fact!" He shoved back from the console, rising to square off against him. "Look, you show up here with your guns and your buzz cuts, but when it comes to actually saving the city, you turn to the scientists. And every time, what you ask is impossible."

"When was the last time you slept, Doctor?"

"Du-du-du-du, shut up, I have an idea."

"The Chair," Zelenka said.

"Of course the Chair. The problem is tying it into the jumper systems."

"Without overloading the generators."

"Possibly using the drones on the jumpers themselves as a means of propulsion."

"While increasing the inertial dampening to maximum."

"They're very good," Alice murmured, drowning out the rest of the conversation. John started to answer but stopped when the pair turned to leave.

"Is that a yes?" Everett called after them.

"No, it's a possibly," McKay retorted.

"I'll take it." To John, he added, "How much damage can one puddle jumper do?"

"I've got an idea about that too. I think I know where we can get another nuke."

Elizabeth straightened, looking disbelievingly at him. "Major, I don't know how sympathetic the Genii will be to our situation."

"The Genii?" Everett repeated.

"They want to test their weapon? Now's their chance."

"Teyla's looking for you," Alice said. "In the Gate room."

John turned to the balcony; Everett followed him, frowning, and they saw Teyla below. "I need to talk to Doctor Weir!" she called up.

"Teyla?" Elizabeth leaned over the rail, gesturing the Marines away from her. "What's the matter?"

"The Wraith. They are in Atlantis."

* * *

"Did we forget the talk about warning me about things like this?" John muttered, letting the noise of the nearest batch of Marines cover his voice.

"Did we forget that most of the sensors are down?" Alice retorted. "I can't see anything without them, remember? You're lucky I'm functioning."

John turned away as Ford came past, talking to Everett. "The Wraith piloting the kamikaze ships beamed into the city right before they hit."

"So they're trying to take the city intact." Everett nodded. "How many we talking about?"

"How many darts crashed?" John asked.

"Between twenty and thirty. And internal sensors are still down."

"Well, we have this." He pulled his lifesigns detector out of his vest pocket, switching it on with a thought. "It can't differentiate between Wraith and human, but if we confine all base personnel to the designated areas, then the blips that show up out of bounds will be the likely targets."

"Let me see that?"

John passed it to him. "Won't do you any good. You need the gene."

Everett held it up. "I got the gene therapy too."

John turned enough to glare at Alice, who spread her hands innocently.

"We wish to help," Teyla was saying. He turned back, glancing at the group of Athosians behind her. "This is quite a large city, Colonel. You need as many people searching as possible."

"She is the one who sensed the Wraith's presence in the first place," John reminded him.

Everett nodded. "Captain, get some weapons for these people."

John grinned at Teyla, who nodded solemnly before turning to organize her people.

"He's learning," Alice murmured.

"Still don't like him, huh?"

"Let him save the City, then we'll see."

"Ready, sir?" Ford asked.

"Yeah. Let's go."

* * *

The hunt went well for a while, all teams reporting kills, and then the power went out again. John halted, one hand going to his radio.

"Wraith killed the generator," Alice offered, a beat ahead of Everett.

"What's the nearest generator station?" John asked, glancing at Ford.

"Number three. Teyla's group is closer."

"Teyla?"

"_We are already on our way, Major!_"

"Meet you there." He gestured to Ford and headed off at a run.

* * *

"The Chair remote for the Gate ship is working," Alice said casually.

"Not the time!" John snarled, firing again. The last Wraith fell and he stepped out of hiding, heading for the generator room.

Teyla met him at the door, gun still in hand. "That should be the last of them," he said. She nodded, turning back to her team.

"And Elizabeth got the weapon," Alice added, a little more subdued.

"Thanks," he murmured.

"But Rodney says it's incomplete."

Giving up, he left the room to talk to her. "How incomplete?"

"Fixable. But maybe not in time. Very close." She glanced up. "One of the Gate ships has seen the Hives."

John nodded quietly. "All right. We need to..."

"_Major?_" Rodney broke in. "_We need you in the Chair room."_

"On my way. Ford!" Ford stuck his head out of the generator room, and John said quickly, "You're in charge. Keep flushing them out."

"Yes, sir. Good luck."

* * *

"Generator's not powering up like it should be."

John shifted on the seat. "Can you fix it?"

"I'm trying!"

"_They're sending in another wave_," Elizabeth warned them over the intercom. "_Major, we need to go!_"

"McKay!"

"There's something wrong. Power levels are dropping."

"_Rodney, nothing is happening!_" Zelenka said anxiously from the 'Jumper bay.

"I know nothing is happening, I'm watching it not happen!"

"_Why are there no 'Jumpers in the air?_" Elizabeth demanded.

"We must have exhausted the Mark II's energy output." Rodney pushed away from the laptop. "It's dead."

John thought quickly, scrambling off the Chair. "So long, Rodney." He was gone before Rodney could process that, let alone stop him.

* * *

"What are you doing?" Alice demanded, doing the bizarre moving-without-moving thing again. John ignored her, skidding into the Control room in time to catch the tail end of Elizabeth's order to evacuate.

"Elizabeth, wait."

"You _can't_," she protested as he headed for the 'Jumper bay.

"I have to, and you know it."

"John..." He stopped, waiting for her, and she nodded reluctantly. "Go."

John brushed past Zelenka in the bay, powering up the 'Jumper almost before he was in it.

"Major?" Zelenka said in surprise.

"Get out of the way, Zelenka," he said quickly, lifting the ramp.

Alice was standing at his shoulder. "I'm supposed to help you protect the City, not commit suicide," she said quietly.

"So help me. Think of another way, fast." She shook her head. "No. Didn't think so. Stay in the City."

"I'm already in the City, John. I'm staying with you."

John hit the atmosphere, flipping the cloak on and turning on his radio. "Hopefully if I take this out, the other will think twice. You know, if this works somebody might have to do it again."

"_Understood_." Elizabeth's voice was soft.

"_You let Sheppard fly that jumper?_" Rodney demanded. John didn't answer; the words were distant enough that he was pretty sure they hadn't been aimed at him.

"_Help me arm the self-destruct in case this fails,_" Elizabeth said after a moment.

John raised his voice. "They haven't detected my approach. Weapon is armed and ready. I'm going in."

The 'Jumper headed straight for the Hive.

* * *

Duchess: I loved Grodin, he was one of my favourite secondary characters...I hated writing those words, but, y'know, you do what you gotta do.

Scarlett: Look, I waited until you were home! :) Enjoy, and htanks for the super long review.

Trecebo: I know! What's a program of a girl to do? :Shrugs:

Aria: Thank you! Glad you're enjoying. Stay with us. :D


	10. The Sige pt 3

Author's note: Things that don't belong to me include characters, situations and large parts of the dialogue.

THE SIEGE 3

Time was telescoping oddly. John was sure he should have reached the Hive by now, but it remained obstinately far away.

His comm switched on unexpectedly. "Major Sheppard, decloak your Jumper immediately."

"What?! Who the hell is this?"

"Not a Hive," Alice said quickly.

"Authentication Alpha Charlie One. Decloak now."

John did, grabbing the lifesigns detector as everything washed white.

When his vision cleared he was standing in front of the viewscreen of a Prometheus class vessel. Turning, he looked at the man in the commander's seat.

"Major Sheppard?"

"Yes," he said cautiously.

"Colonel Steven Caldwell."

"Thanks for the rescue."

Caldwell nodded. "We're attempting to contact Atlantis now."

"What about the Hive?" He glanced at the life signs detector, still gripped tightly in one hand.

"Your target was destroyed." He glanced back at a signal from one of his crew. "We've raised Atlantis. Go ahead."

John turned back towards the viewscreen. "Atlantis, this is Sheppard."

_"John?"_ Elizabeth demanded.

"What other Sheppards do you know?"

He heard Beckett, in the background, breath a relieved, _"Oh my God!"_ and Rodney protest, "_No, no, that can't be. We saw the hive ship go up."_

"I assure you, Doctor McKay, that Major Sheppard is alive and well," Caldwell said.

_"Who is this?_" Elizabeth asked.

"Colonel Steven Caldwell, commander of the _Daedalus_. We are ready to assist you."

_"Oh, thank you!_" Rodney said.

_"We are very glad to hear it, Colonel_," Elizabeth said. _"And I assume we have you to thank for saving Major Sheppard."_

"We were monitoring your transmissions as soon as we came out of hyperspace. We couldn't beam him in until he decloaked his Jumper."

"Didn't take much convincing!" John told her.

"Doctor McKay?" Caldwell asked.

_"Present, yes."_

"I trust you'll know what to do with this?"

He gestured to one of the crew, adding to John, "We're beaming down the ZPM."

"You've just made a friend for life. Or until Rodney gets distracted by something else."

"_How did they do that?_" Carson asked in surprise.

"_Well, the _Daedalus_ is loaded with Asgard technology. The beaming technology's the first part of it. They've got things like ..."_

"Rodney," John said quickly. "What say we get the shields back up?"

_"Yeah,_" Rodney agreed dazedly. _"What say we?"_

"_We still have Wraith all over the city,"_ Elizabeth told them.

"After we deal with this other hive ship, we'll assist you as soon as we can. Caldwell out."

"Sir, we have incoming enemy fighters bearing three-two-zero," one of the officers said.

"All forward rail guns stand by. Launch all fighters."

John turned back towards the viewscreen, watching the battle. The fighters weren't visible yet, but he could see the shields flaring each time they were hit.

He glanced around when the intraship comms came on. _"Colonel Caldwell. This is Novak in Engineering."_

"What is it?" Caldwell asked.

_"Uh, Hermiod wanted to remind you that that our shield strength will be severely diminished without the Zero Point Module tied into our power systems."_

"I'm well aware of that, Doctor. Caldwell out. Major, do you recommend any specific target on the hive ship?"

John blinked, realizing a second too late that Caldwell was talking to him. "One of the fighter bays, sir."

"It would increase the chance of secondary explosions."

"That was the thinking, sir."

"I agree. Weaps, arm two Mark Eight tacticals. Our target is the hive ship's main fighter bay."

"Warheads armed...target is locked, sir."

"Fire."

Several Darts managed to deflect the warheads; they impacted harmlessly against the Hive's shields.

"We need to get in close," John advised him.

"Helm, alter heading to intercept. Go to max thrust."

"Max thrust," the Helm officer repeated.

"We just need to get closer," Caldwell muttered.

"The Asgard gave you hyperdrives and shields. How come no offensive weapons?" John asked.

"They don't like providing other races with anything that could potentially be used against em."

"I thought they were allies."

"Without the beaming technology, you wouldn't be here, Major. Arm two more Mark Eights."

"You're wasting ordnance, Colonel. Those missiles are being intercepted miles from the hive ship."

Caldwell ignored him, gesturing for the weapons officer to fire anyway. Again, the warheads were destroyed harmlessly.

"Well, now we're 0 for 2," John remarked. "How many of these things have you got?"

"Only one needs to get through," Caldwell pointed out.

"Is there any way we can deliver a warhead the same way you plucked me out of the Jumper?"

"The Asgard have already considered that, Major. There are failsafes built into the system to prevent their use as a weapons delivery system."

"You've got one of these Asgard on board? Can he override the failsafe?"

"Why would he do that?" Cladwell protested.

"Well, his butt's on the line just as much as ours."

Caldwell nodded slowly, reaching for the comm. "Novak, I need you and Hermiod to figure out how to get a site-to-site transport lock on a set of co-ordinates inside the hive ship."

_"No-no-no-no-no-no. Sir, Hermiod isn't gonna like that."_

"Get it done, Doctor, that's an order."

It took longer than John was comfortable with, but eventually Novak contacted them. _"Colonel? Hermiod is ready and standing by for warhead transport. But I can tell you, he is not happy about this!"_

"I'll take that under advisement. Are we within transport range?"

"Yes, sir," his weapons officer said.

"Transport warhead when ready."

_"Ready. Five..."_ She stumbled over the words, correcting herself to say, _"The weapon is away."_

John turned back to the viewscreen, watching as the Hive tore itself apart.

"Novak, I need you to prep another warhead for transport," Caldwell said. "We need to take out those cruisers."

"Sir, wait." John glanced back out as the cruisers jumped into hyperspace.

"Colonel, cruisers have broken off and entered hyperspace," one of the officers confirmed.

"Seeing what we just did to their remaining hive ships, I don't blame em."

"There's still a lot of Darts out there," John reminded him.

"Alright, let's clean this up," Caldwell agreed.

"Sir," one of the officers said. "The remaining fighters are regrouping."

"Alright, take position, stand by for defensive fire."

"We're not the target," John muttered.

"Major Sheppard is right, sir. The formation is headed toward Atlantis."

John raised his voice. "Elizabeth, you've got a problem."

_"Yeah, we see that, Major."_

"We're moving to intercept but I don't think we can get there in time." John glanced back at Caldwell, who shrugged.

"Not a chance. They're coming in too fast."

_"Oh my God. Their approach is ballistic,"_ Zelenka said.

_"What exactly does that mean?"_ Elizabeth asked.

_"Their impact velocities will be in excess of ten thousand kilometres an hour. No part of the city can withstand that."_

"You'd better get the damned shield up!" John warned them.

_"How much time do we have?"_ Elizabeth asked.

_"Forty-five seconds,"_ Zelenka answered distractedly.

_"Rodney, we need a shield up in forty seconds or we're dead!"_

McKay and Elizabeth bickered about it for several seconds; John listened to the familiar patter, watching the viewscreen. Finally, just past the point of too late, the shield went up and the Darts smashed into it, exploding.

"Atlantis, this is Sheppard, come in." He glanced at Caldwell when no one answered. "Atlantis!"

_"We're still here,"_ Elizabeth said finally. _"That's our status."_

"Don't scare me like that!" John protested.

_"Sorry. What about the Wraith fleet?"_

"The remaining cruisers have withdrawn from the battle," Caldwell told her.

_"Thank you, Colonel. Thank all of you."_

"Glad to be of help. We're gonna stay in geosynchronous orbit for the time being. Can we be of any further assistance?"

_"We could use some help with the Wraith in the city."_

"We'll send in some people to help with that. _Daedalus_ out." Caldwell glanced at John. "Major Sheppard – I'm sure you're anxious to get back to Atlantis."

"Yes sir. Thank you."

* * *

Caldwell detailed three Marines to go down with John while he sorted out the rest of the teams. Hermiod, still grumbling about the misuse of his systems, sent them directly into Stargate Operations, right into the path of one of John's soldiers. He noted with pride that the man had them covered, but backed off on recognizing them.

"Secure Stargate Operations," John told the marines. They split off as Elizabeth came down the steps from the gallery. "Well, I'm home!"

Elizabeth hugged him. Jon blinked, surprised, and rather tentatively hugged her back. After a moment she let go, drawing back to look at him.

"Yes, you are. I truly thought..."

"Yeah, yeah, I thought the same thing about you a minute ago. We gotta stop that!"

"I'd like that," Elizabeth agreed.

"So, uh, where are we?" John looked around, noticing Alice waiting patiently near one of the corridors.

"Well, most of our sensors are still down, but we do know there are at least a handful of Wraith still in the city," Elizabeth told him.

"Still got some work to do."

"Before you do anything, Colonel Everett insists on speaking with you. He's in the infirmary."

John nodded, heading towards the infirmary. Alice paced him, waiting for him to speak first.

"Had fun while I was gone?" he asked.

"Same old, same old," she agreed. "John, I don't know how much help I can be. A lot of sensors are down."

"Stick around anyway." He pulled the life signs detector out of his vest. "Get everything you can?"

"Yes. Your ship's very big. The computers are funny, though. They're not like the ones you brought from Earth."

"They're made up from different systems the SGC found. A bit of Goa'uld, a bit of Asgard. Think there's some Tok'ra in there." He shrugged. "You can still read them, right?"

"I'm Ancient built. I can read anything your people can design."

"Good to know that humility thing's really working for you." John glanced down the corridor at the infirmary, halting. "Look, what kind of shape is the city really in?"

"Not so bad, really. A lot of circuits burned out. Mess and dirt. Nothing really structural damaged."

"And the ZPM?"

"Shields for a while. Dial to Earth, maybe. Other systems for a while. It's not at full power."

"Figures." He looked towards the infirmary. "You know why Everett wants me?"

"No. Only that he's insistent. The Wraith almost killed him."

John blinked, glaring at her. "He was attacked? And you're mentioning this now?"

"Almost drained. But still alive. He'll live to wish he wasn't."

John grimaced at that, turning and heading for the infirmary.

* * *

Much later John came back to the Gateroom, talking to Zelenka. "Preliminary count is forty casualties, maybe more. I'm still trying to line up lifesigns readings with actual people."

"There are no Wraith lifesigns?" he asked, glancing up as Elizabeth joined them.

"The last one was trapped in one of the deeper parts of the city," Zelenka said absently. "He died trying to damage city with one of their grenades."

"Three of our men were injured," Elizabeth added. "On the bright side, there was no flooding."

"Have we been able to locate Lieutenant Ford yet?"

"I'm sorry, no. We've searched everywhere in the city. It's possible he may have beamed up into one of the Wraith Darts."

"Let's not make that assumption here." He glanced around, catching Alice's eye.

"Major, I'm sorry – we've searched everywhere inside the city."

Alice paled. "He's in the water. John, he's in the water just outside the city."

"Well, how about outside the city?"

"I don't understand." Zelenka frowned.

"Well, expand the sensors. Maybe he's in the water."

"Even if that was the case, there's no chance that ..."

"I'm not asking you to swim out there, I'm asking you to press a few damned buttons."

"Hurry," Alice murmured.

Zelenka turned to the console, changing the settings. "Even if you're right, I don't see how...Oh my God."

The screen clearly showed a lifesign, just outside the shield. John half-turned, looking at Elizabeth, who was already touching her earpiece.

"Colonel Caldwell? One of our men is in the ocean outside our shield, most probably injured. Can you beam him to your ship and then down to our infirmary?"

There was silence for a moment until they heard, _"Atlantis? This is Doctor Novak on the _Daedalus_. You're gonna need some SFs in your infirmary before we beam your man down."_

_"We already do, Doctor,"_ Carson told her. _"Beam away."_

Alice made a face. "There's a Wraith."

"It's a Wraith?" John said through gritted teeth.

"No. It's Ford. But there's a Wraith too." Catching his look, she added, "A dead Wraith. But still a Wraith. I hate them."

"You're not the only one." Louder, he added, "I'm gonna go check on him."

"Right," Elizabeth said absently.

* * *

Carson was busy when John got down there; he paced for a while until one of the nurses threw him out, and then went on a round of the city, checking in with as many of his men as he could find. Eventually Alice appeared to tell him Ford was out of surgery, and he excused himself and went back to the infirmary. Elizabeth caught up to him just as he reached the door, and Carson redirected them into his office.

"I gave him a mild sedative to help him rest," Carson told him, "but he should be dead."

"Well, he's a tough kid."

"Not my point, Major. He was lying face down in the freezing water for over an hour. I don't care how tough he is."

"So what are you saying?" Elizabeth asked.

"We still have no idea how it works, but during the Wraith feeding process, the victim is injected with a special enzyme. It strengthens the human body temporarily and ensures that the heart continues to beat."

"Why would they wanna make you stronger?" John protested.

"Cos when you die, it spoils their fun," Alice told him, drowning out Carson as he said essentially the same thing. John scowled at her, wishing he could tell her to get off Carson's desk.

As though sensing his thoughts, she grinned and swung her legs.

"They make you stronger so they can take more time to kill you," Elizabeth summarized.

"Lovely, isn't it?" Carson agreed. "In most cases the enzyme is released slowly into the bloodstream throughout the feeding process. I can only ascertain that the Wraith died quite suddenly and that Lieutenant Ford's system became flooded with it."

"And that's why he was able to survive in the water for so long."

"Exactly. The problem is, now the enzyme is breaking down in his system. Eventually there'll be none left."

"Well, that's not good."

"No. In fact, I'm quite certain it'll kill him. It's possible his body's become dependent on the enzyme to function."

"Your doctor's really very smart," Alice said. "Ours never figured that out. Although we tended to kill the Wraith before they ever made it into the City."

John glared her into silence; he'd caught the gist of what Carson and Elizabeth were saying under Alice's words. They were talking about weaning Ford off the enzyme.

"Then we're gonna have to get more of this enzyme," he said.

"Aye. With your permission, Doctor, I'd like to harvest it from the Wraith bodies in the morgue. I know it's a wee bit creepy, but..."

Rodney broke in over the radio. _"Elizabeth. Major Sheppard."_

"Do whatever you have to do," Elizabeth told Carson. "What is it?" she added to Rodney.

_"You're gonna want to get up here."_

John grimaced, turning to follow Elizabeth out.

* * *

Rodney and Radek were both working on laptops, yelling back and forth at each other in scientist's shorthand.

"Aren't you supposed to be getting some sleep, Rodney?" John asked.

"I was trying to do just that, but _someone_ thought I should know the deep space sensors were back up and running." He glared at Radek, who glared right back at him.

"Yes? And?" Elizabeth said pointedly.

Rodney turned back to his laptop, leaving Radek to answer.

"We've picked up twelve more hive ships traveling in hyperspace."

"Their course and speed will bring them here in thirty-six hours," Rodney added.

Elizabeth sighed, rubbing her face and pushing her hair back. "Alright. Get Colonel Caldwell down here."

"I'll be back in a second," John said, stepping into the corridor. "Alice!" he hissed, frowning when she didn't appear. "Ok, I'm pretty sure there's no Ancients in the City right now. What are you doing?"

She still didn't appear, and he could hear Caldwell's voice from Operations. Giving up, he went back to join the meeting.

"Twelve hive ships?" Caldwell demanded.

"The cruisers that got away probably called for reinforcements," John told him.

"Our research shows there are at least sixty hive ships in this galaxy," Rodney added. "I mean, who knows how many more could be on the way?"

"At least the shield's up and running."

"That only buys us time."

"I like time!" John protested.

"Look, the first siege of Atlantis lasted for years. I mean, with only one functioning ZedPM, we can't expect to hold on that long."

"Can we submerge the city again?" Caldwell asked, apparently tired of being ignored.

"It's a city, not a yo-yo. Look, I don't even know how they did it the first time."

"How long until they arrive?"

"A little over a day," Elizabeth told him.

"You know what?" John sat upright. "I'm sick of this."

"I'm sorry?" she said in surprise.

"I mean, sitting around waiting for them to show up. I say we take the fight to them."

"We've got _one_ ship, Major," Caldwell reminded him.

"We've got one ship with an Asgard shield, an armoury full of nukes, _and_ beaming technology. That evens the odds a hell of a lot."

"Twelve ships and their escorts."

"I'm telling you, we've gotta send these guys a message. We're not like the Ancients – we're not gonna sit around and wait. We don't back off – we have the capacity and the will to go kick their asses for a change."

"How do I fight a ship in hyperspace?" Caldwell protested.

"The Wraith faster-than-light travel is not as efficient as the Asgard hyperdrive aboard the _Daedalus_," Rodney said, turning on a nearby screen. It was displaying the fleet's path. "Not only are they slower – they need to travel in a series of jumps. So, if my calculations are correct, they'll make one last stop here, fifty light years away, before they make the final jump to Atlantis."

"Doctor Weir?" Caldwell asked.

Elizabeth frowned, looking at John. "It will feel good to have them on the defensive for a change."

"Alright then. Let's do this."

Before he left John tried to find Alice again, but she was still mysteriously absent.

* * *

The attack, good in theory, didn't stand up to the engagement and the damaged _Daedalus_ landed on one of the piers. John led Caldwell and a couple of other officers into the City, watching out for Alice who was still MIA.

Elizabeth met them just inside the City. "Welcome back to Atlantis, Colonel."

"The Wraith are right behind us," John told her.

"I wasn't expecting you to land."

"Until repairs are complete, the _Daedalus_ is gonna need Atlantis' shields as much as you do."

The comm went off abruptly. _"Doctor Weir – the hive ships are emerging from hyperspace."_

"We're on our way."

They met Rodney on the way, piling into the Operations room together. Alarms were going off as Rodney shoved he nearest tech out of his seat.

"They're getting into some sort of formation," someone else said.

Shots began to echo from above and everyone automatically flinched, looking upwards as though they could see the shield from where they stood.

"The shield's holding under the bombardment but it's under incredible strain." Rodney stared at his screen.

"How long will it hold?" Elizabeth asked.

"Well, if they stop firing it'll last almost indefinitely, but..."

"Are we talking months, weeks?" she interrupted him.

"Days. At this rate the ZedPM will be depleted within days."

* * *

Much later Rodney stood with John on the balcony, watching the blasts impact against the shield.

"It's almost pretty, isn't it?" Rodney said reflectively.

"Almost – but not quite." John glanced around, but Alice was still missing.

Giving up for the moment, he headed for the conference room with Rodney. The others were already there.

"The _Daedalus_ will be back in fighting form within the next twenty-four hours," Cladwell told them, "but I think the next engagement's gonna have the same result."

"Even if we were able to destroy these ships this instant, more would be here in a few days, and even more a few days after that." Elizabeth shook her head. "From where I'm standing, I just don't see how we can win this."

"Well now we know how the Ancients must have felt."

Radek shook his head. "Atlantis is only way to Earth. As long as they know we're here, they're just going to keep coming."

"As long as they know that we're here," John repeated slowly.

"What do you mean?" Elizabeth asked.

"Zelenka just said as long as they know that we're here, they'll keep coming."

"Yes, he said that," Rodney said irritably.

"Well, what if they thought we were gone?"

"Then there would be no reason for them to stay," Teyla realized.

"Exactly!"

"Exactly what?" Rodney protested.

"We disappear."

"Destroy the city, you mean?" Caldwell frowned.

"No, we just make it _look_ like we did."

"How?"

"We cloak it," Rodney said in sudden realization.

"Yes," Radek agreed. "Yes! The Puddlejumpers are equipped with cloaking technology which renders them invisible to the naked eye, and to Wraith scans. If we just simply remove one of the cloak generators from the Puddlejumper..."

"I wouldn't say simply, but yes – by interfacing a Jumper's stealth cloak generator with the city's shield, we should be able to render the city invisible."

"That's all well and good, but I think if the city were to suddenly disappear, they might be able to put one and one together," Caldwell pointed out.

Rodney nodded impatiently. "Which is why we fake a self-destruct. Have the _Daedalus_ beam a nuke right above the city's shield, and then detonate it. While their sensors are blinded, we cloak the city; when the smoke clears ..."

"... nothing but ocean," Elizabeth finished.

"What about hard radiation?" Caldwell asked.

"I should be able to calculate with reasonable accuracy how long to wait until we switch over to the cloak."

"But what about the displacement issue?" Radek protested.

"It's coparambulation – that's the easy part!"

"OK," Radek agreed. "What about the hard part?"

"Hard part?" John said sharply.

"Um..." Rodney busied himself with his computer. "The cloak for all intents and purposes will replace the shield, which means that we'll be completely unprotected once the cloak's activated."

"We'll be completely exposed?" Elizabeth repeated.

"Well...yes."

"So if they're not fooled by the ruse..."

John finished Caldwell's sentence. "...then they destroy the city – which, I remind you, is exactly what we were gonna do anyway."

"What about the _Daedalus_?"

Caldwell grimaced. "Well, if it doesn't work, our shields should be sufficiently recharged to break through their lines and escape. We know we can outrun 'em."

"Alright," John said quickly. "Let's get as many non-essential personnel on your ship as we can – just in case."

"I love this idea," Elizabeth said slowly. "I really do – _but_ the Wraith are aware that we have cloaking technology."

Teyla rose. "They are close – close enough for me to connect to them. If I can convince them that we intend to destroy Atlantis rather than allow it to be taken, just before the explosion occurs..."

"How will we know whether or not they believe you?"

"Well, if they stop the bombardment, we'll know," John suggested.

"He's right. If the Wraith believe that we intend to destroy the city, the last thing they will want to do is to help us do it."

Elizabeth nodded, turning to Rodney and Radek. "How much time do you need?"

"Oh, well..."

"...a week..."

"...a couple of hours..."

"I'll take the second estimate. Go."

* * *

Carson met them on the steps outside, out of breath. "He escaped."

"What?"

"Who?" John demanded, overriding Teyla.

"Lieutenant Ford. He was able to disarm one of the marines, and got away with all the Wraith enzyme I had left."

John tapped his comm. "Ford, this is Sheppard, come in...Ford? I need you to come back to the Control Room, buddy, we're all goin' home."

Ford didn't answer, and John glanced at Elizabeth. "Lieutenant, do you copy?"

_"You're just afraid of me, Major. You're afraid of what I can do now. I'm not listening to you."_

"Radio's off," Alice murmured. John glanced briefly at her before turning to catch Elizabeth's eye again.

"I'm going after him."

"Now's not the right time!" Elizabeth called, but he was already gone.

"Where have you been?" John demanded.

"The ZPM and your generators are fighting each other, causing some hiccups. I was in involuntary shut down while the fluctuations evened out. Ford's three levels above you."

"You couldn't have warned me?"

"Involuntary," she repeated. "I didn't know it was going to happen."

"That going to happen often?"

"Can't tell, I'm afraid."

"Something you don't know?"

"It's your primitive power sources. He's heading for the transporter."

"Yeah, I got him." John waved his life signs detector.

* * *

Alice drifted along beside him as he tracked Ford through the City, keeping him up to date with Teyla's attempts to contact the Wraith.

"She know you're there?" he asked quietly.

"It's possible. I can't affect anything beyond the displays, and there's too many people around for me to do that unless you really need me to."

"No. Don't..."

"Shush."

John fell silent, slipping behind a pillar. A moment later Ford came around a corner, trotting towards him. John waited patiently, but just before reaching him Ford slowed, apparently thinking for a moment before turning and heading in a different direction.

John stepped out when he was sure Ford was far enough away. "How is he tracking me?" he murmured.

"Who knows." Alice was glaring after him.

"What's up with you?"

"He's part Wraith now, effectively. If my sensors were working properly, he'd be setting off all the alarms."

"Get over it," he told her. "Program yourself not to care."

"I can't, it conflicts with a primary directive. Sorry." She glanced away, smiling suddenly. "They've stopped firing."

"Good," John murmured. "How's the ZPM?"

"Not nearly as strong as it was."

"I could have told you that. How much longer?"

"Will it hold out? Depends on what you ask of it, John. I don't think it'll dial Earth, anymore."

"Doesn't matter, not if the _Daedalus_ makes it through."

John's radio activated, and he paused to listen to Elizabeth. "_Attention all personnel: prepare for detonation flash."_

"I in trouble here, Alice?"

"No, you're not near enough a window to catch the blast. Turn off the detector, though. Just in case."

John glanced down at it, flicking it off. "What's happening?"

"Bombs away." She was standing with her head tilted as though listening to something. "Dr McKay's about to...cloak's on. We're being scanned." She turned to look back at John. "Ford's getting away. You need to move."

"Yeah. Where?"

"One level down, section J four."

John made it in only a couple of minutes, stepping out into one of the open areas that littered the City. Ford was waiting for him, gun aimed and ready.

"I could have shot you a couple of times by now."

John lowered his stunner, letting it hang at his side. "Well, I'm glad you didn't. Look, why don't you and I just go someplace where we can talk?"

Ford lowered his gun, backing up a couple of steps as John approached him. "You're trying to change me back."

"No," John said quickly. "I'm just tryin' to help you."

"Careful," Alice warned. "He's not in his right mind."

Ford shook his head. "No you're not." He turned to leave.

"Oh, crap," John whispered. He raised his stunner, shooting Ford in the back. Ford stumbled but didn't fall, catching himself on the frame of the transporter room and turning to glare at John. He stepped backwards, letting the doors close.

By the time John got there he was gone.

"Damn!" he hissed. "Alice, where's he gone?"

"Operations tower."

John stepped into the transporter, stepping out just in time to see the Stargate begin to dial and a 'Jumper lowering into place.

"Where's Ford?" he called to McKay.

"I assume that's him in the 'Jumper."

John ran down the steps, pausing level with the 'Jumper. He could see Ford inside, determinedly ignoring them, and Alice standing behind him.

"Can they detect that?" Elizabeth asked.

"I don't know," Rodney said absently.

"Shut it down!"

"I can't – the 'Jumper's in control."

"Ford!" John called. "Stand down! This is a direct order!"

Under his breath, he added, "He can hear me, right?"

Inside the 'Jumper, Alice nodded. Beside him, she said, "He can hear you. He just doesn't care."

Ford lifted his gaze to stare at John for a moment before turning away. The 'Jumper turned, picking up speed as it headed into the 'Gate, which shut down behind it.

"Where the hell is he going?" John demanded.

Alice started to answer, but cut herself off as Weir said, "It won't matter if the Wraith can detect the Gate activity through the cloak."

"There's only one way to know," Rodney said, sitting back and looking upwards.

"They're leaving," Alice murmured.

The comm. activated, and Caldwell said, _"This is _Daedalus_. Our sensors indicate the Wraith fleet is breaking orbit."_

Rodney looked down at his laptop. "I can confirm that. They're headed for hyperspace. Look, I'm gonna keep the cloak up for a while just to be sure, but, uh, I think they bought it."

Elizabeth came down to join John in front of the 'Gate. "The Gate address'll be in the log," she offered. "There's still a chance..."

"It doesn't matter where he goes. The second he gets to wherever he's going, he's gonna ditch the Jumper, turn around, and dial another address – one we can't trace."

"We'll find him."

"Maybe."

"Hey." She bumped his shoulder lightly. "At least we're still around to try."

"Yeah." He turned away, heading out to walk the City.

* * *

"If we find the 'Jumper," he said eventually, "can you tell where he dialed?"

"If he used the 'Jumper controls, yes, but you trained him better than that. Dr McKay might be able get it from the crystals."

"No, he'll just go to a trade planet with a lot of traffic." John grimaced.

Alice glanced around. "City's still standing."

"Yeah. More or less."

"Enough. It's been a long time since the City won a fight against the Wraith."

"It's not the end," he reminded her.

"No. But now they know you'll fight." She grinned. "The City will stand with you, John."

"Good to know."

Alice smiled, fading out, and John kept walking the boundaries of his City.

* * *

Duchess: Yeah, I hated him too. He came good in the end, though.

Aria: Thanks. Glad you enjoyed.

Rittanicus: It's good to hear I'm not overdoing it. I can't usually write humour unless it's full on parody, so I'm glad I'm hitting the balance here.

Iniysa: Hope I hit the episodes you're looking for...I'm not doing all of them. Glad you're enjoying.

Kary666: Next chapter is...oooh, now. Enjoy.


	11. Runner

Author's note: Just a tag, this time, because they very annoyingly spent the episode off Atlantis. Things that don't belong to me include characters and situations.

The next chapter's kicking my ass. Sorry this has been so long.

Runner

This day had been far too long already, and it wasn't over yet. Ronon was settled for now; John had made his own report and was now compiling the reports of everyone else who had been on the team.

"Sir?" Major Lorne tapped on his door frame. "My computer shorted out while my report was sending. It get to you alright?"

John glanced at the screen—currently showing a half-finished game of FreeCell. "Your report?"

"Came through five minutes ago," Alice reported, swinging her legs. "It's intact."

"Yeah, it came through," John said, glancing up. "You alright?"

Lorne blinked, rocking back. "Yeah, I just…I thought I heard something. Someone down the hall, probably."

"Thought you heard something," John repeated, glancing briefly at Alice.

"He has the gene. He may be hearing me," she said, sounding far too interested for John's peace of mind.

"That happen a lot?" he asked.

"No sir."

"Just here in the city?"

"In the 'Jumper, earlier." He shrugged. "My radio's probably mistuned. I'll get someone to look at it." He started to turn away.

"Yah!" Alice yelled, and he halted, glancing around. "He's definitely hearing me, John."

"Why isn't he seeing you, then?" John wondered.

"Sir?"

"Sit down, Major. We need to talk."

It was the first time he'd tried to explain it, really; Teyla had accepted without understanding, and he hadn't realised exactly how insane it sounded.

"…Atlantis talks to you."

"Not Atlantis. Exactly. A program, a research program."

"A research program…that manifests itself as a blonde girl."

"Yes."

"That only you can see."

"Yes."

"And I can…hear. Sometimes."

"Apparently, yes."

"But Dr McKay has the gene."

"Artificially. I'm told that's not as strong. Major, you must have seen stranger things at SGC."

"As strange, anyway." He glanced around. "She here now?"

"Yeah. She doesn't get to meet new people much."

"Meeting them isn't a problem, it's interacting that tends to slow things down," Alice pointed out.

Lorne was frowning. "Something…something interacting something?"

"Well, that's not going to be much use," Alice muttered.

"I heard _that_," Lorne warned her. He looked back at John. "And no one knows about this?"

"Teyla. Sort of. It's not the kind of thing you put in the leaflet; 'Your Commanding Officer may pause to consult invisible beings from time to time.' "

"I'm not invisible," Alice protested.

"Effectively, y'are." He looked at Lorne. "You're not hearing things."

"She sees everything the scanners do?"

"A lot of it's under privacy lock, but yeah. Internal and external. Unless they're malfunctioning."

"I can't do anything about malfunctions! I can't affect the wiring or the power supply. You know that."

John shrugged innocently. "I didn't say anything."

Lorne rose to his feet. "I should let you two talk."

"Yeah."

"I like him," Alice said, deliberately loud. Lorne slowed, grinning over his shoulder before heading out.

"Suck up," John accused her.

"Yes," she agreed. "Of course I'm sucking up to the guy who hears one word in three and can't see me at all. I'm tired of being understood all the time. Takes the fun out of everything."

"Definitely…"

"Too much time in McKay's computer," she recited, rolling her eyes. "Yes, so you keep telling me."

"Shame you're not learning, isn't it?"

"I'm learning how to lose at FreeCell."

"Life skill, that."

"Apparently, yes. How did you correlate your reports before I started doing them for you?"

"That's delegation! Important for any leader."

Alice grinned, hopping down from his desk. "More or less important than losing at FreeCell?"

"About equal. Hey? Keep an eye on Lorne for a bit."

She nodded, turning away and vanishing midstep, and John settled in to read the last couple of reports.

TheNaggingCube: You should enjoy this one, then.:)

Duchess67: gotta make it make sense, though. But you should enjoy this one! No unecessary bits. :)

Aria: Yeah, poor old Ford. Never mind, he'll be back eventually.

Babyurl: Thanks! Glad you're enjoying.


	12. Trinity

Author's note: Things that don't belong to me include characters, dialogue and events.

* * *

TRINITY

* * *

"Doranda," Alice said thoughtfully. "I haven't been here in years."

"You haven't been anywhere in years," John reminded her softly.

"No, I mean even before the People left."

He nodded, glancing up and interrupting Rodney and Ronon's discussion. "McKay. Are you reading anything?"

"Nothing. Life signs from the planet are negative."

"Then it is a shame." Teyla leaned forward to look out the windscreen. "From what we read in the Atlantis database, the Dorandans were a wonderful race of people."

"Well, the database is over ten thousand years old," Rodney reminded her. "You can bet things have changed around here."

Ronon rose suddenly, squinting. "Sheppard."

"Oh," Alice said in surprise.

"OK. That's not something you see every day," John murmured.

A field of debris lay outside, spinning into a ring around the planet. John slowed, easing them in and watching carefully.

"There was a great battle here," Teyla said thoughtfully.

"Hive ship," Alice said suddenly.

"That is a hive ship," Teyla said at the same time.

"That was a hive ship," Ronon corrected her.

"Something put a lot of holes in it alright. We should check it out."

"Whoa-whoa-whoa-whoa-whoa," Rodney protested. "What if whatever put the holes in it wants to put holes in _us_?"

"Well, you just said, a lot's changed in ten thousand years."

John glanced at the HUD; Alice nodded. "No life signs. There's nothing here, John."

The 'Jumper broke the cloud cover and John sighed at the sight of a city in ruins below them.

"That would explain the lack of life signs," Rodney said, slightly subdued.

"This is what usually happens when you fight back," Ronon told him.

"These folks took out a fleet of Wraith ships," John protested. "I'd say they did a pretty good job of fighting back."

"Hold on." Rodney poked at his panel. "I'm picking up faint energy readings coming from...there. That would explain how they were able to put up such a good fight."

"How?"

"Because...they were Ancients."

* * *

John let the others out of the 'Jumper ahead of him, fiddling with his equipment. "Alice?" he said tightly.

"Yes, John."

"You didn't tell me this was here because...?"

Alice glanced around. "Because I didn't know. John..." She hesitated, face changing. "Oh."

"Oh, what?"

"Oh. Nothing. Your team's waiting."

"Why didn't you know this was here?"

"I'm only a Gate Ship program. Atlantis may have more information. Or you can ask in the installation."

"The installation has an Alice program?"

She grinned. "It does."

"John?" Teyla asked from the ramp.

"Coming." He glared at Alice. "We're gonna talk later."

"Yes sir."

* * *

John followed the others down a ladder into a laboratory. Apart from the dust and the lack of clutter, it could have been any lab in the tech suite on Atlantis; the console layout was exactly the same.

He wandered around the room, waiting for Rodney to get the power up. "I got two bodies here," he noted.

"I got three more over here," Ronon added from a side passage. "Whatever happened here, no-one came back to claim the dead."

"Can't tell if they were fed on by the Wraith," John muttered.

"Yeah, well something killed them."

"Something killed everyone on this world," Teyla reminded them.

"Now why is this outpost – if that's what it is – still intact? Doesn't make sense. What do you think, Rodney?"

The lights powered up and his ATA tingled, suddenly aware that it was surrounded by Ancient tech.

"Ha!" Rodney grinned. "Sorry, I wasn't listening, but it just struck me that, if this is an Ancient outpost, why would the Wraith leave it intact?"

John took a deep breath. "It's a good question."

"Huh." Rodney turned back to the console.

When nothing else seemed to be forthcoming, John took up a patrol of the room. The consoles continued to flicker as he walked past them, but apart from Rodney's stream-of-consciousness muttering, the room was silent.

And then the ATA lurched and he turned to see an elderly woman watching him.

"Alice," he said under his breath.

She shook her head. "Arcturus."

John raised his voice. "Teyla? I'm gonna poke around a bit. You guys stay here."

"Want company?" Ronon asked.

"No. I'm not going far." He gestured vaguely down the passage. "See if there's any more bodies."

Teyla nodded and Ronon turned away; John headed down the corridor, following the curve. "Arcturus?"

"Your Gate Ship tells me I should respond to Alice, also."

John eyed her. "Maybe not. What happened here, Arcy?"

She smiled faintly at the nickname. "The People found a new weapon. But too near the end of the War. No time to be sure, no time to check...all went wrong. The Wraith came."

She was flickering in and out as she stood there. John blinked, frowning. "What's wrong with you?"

"Not much power left. It goes to essential systems first."

"And you're not an essential system. Right. What about the weapon?"

"Never worked right. Pulled too much power. Not enough time to understand it...abandoned, attacked. All finished."

John nodded slowly. "Is it fixable?"

"They couldn't do it." She tilted her head, studying him. "Alice thinks you can."

* * *

Teyla accidentally on purpose dropped her pack as they were preparing to leave; Ronon stopped to help her gather her stuff together, and Rodney took the opportunity to get some extra readings. John grinned at her, swinging up the ladder and making for the 'Jumper.

"Alice!" he called as soon as the hatch was open.

"Yes, John?" She stepped out of the cockpit, eyeing him.

"Your cousin down there's a little crazy."

"My cousin down there's a little shellshocked," she corrected him.

"She's a program!"

"Yes." She studied him for a moment. "What did she tell you?"

He gestured vaguely, sitting to begin the preflight. "That there was an attack."

"Yes?"

"That's it. Weapon never worked, then there was an attack."

"She wasn't turned off."

John's hands fell from the board. "What?"

"When the attack came. It was sudden, they weren't expecting it, and she wasn't turned off. Everyone died or left and she wasn't turned off. The power didn't run down for centuries."

"Why didn't she turn herself off?"

Alice smiled bitterly. "We couldn't do that then. Your crew's coming."

"You're telling me the computer down there is insane?"

"Not insane," Alice said impatiently. "She's a program, she doesn't go insane. But her internal logic is not always consistent."

"Sounds insane to me," John muttered, glancing up as the others spilled up the ramp. "Took you long enough!"

"Is everything well?" Teyla asked warily, sliding into the seat behind him.

"Enough for now, anyway. McKay, you ready?"

* * *

Elizabeth was waiting in the control room when they came down from the 'Jumper Bay; Rodney was already talking before he'd hit ground. John caught Elizabeth's eye, shrugging minutely; they'd both developed the ability to ignore most of Rodney's speeches while still catching the important parts.

"So it's a military research facility," Elizabeth said finally.

"From what we can tell, it's a ground-based version of the satellite weapon we used to destroy that hive ship," John explained.

"That sounds right," Alice agreed. John tilted a glare at her, ignoring Rodney's expansion of the weapon's destructive power.

Elizabeth finally agreed to send a team back, mostly to stop Rodney from complaining at her for the next month.

"We'll leave in the morning," John told him. "Brief your team and get whatever you need."

"Yes, oddly I _do_ know how to do it, thank you very much." Rodney brushed past him, one hand on his radio. "Zelenka! Drop whatever you're doing, I've got a new project. It is so more important than yours! Hey, I know what that means."

"Good luck," Elizabeth murmured, turning to head into her office.

John headed for his quarters, waiting until he reached the transporter to ask, "Can it be fixed?"

"Maybe. Arcturus couldn't figure it out, but her work was all theoretical. And you have a very good record."

John grimaced. "How come the Ancients couldn't figure it out?"

"Not enough time. Too ambitious a project, maybe. Several of the files are missing, it's difficult to reconstruct. And there's no mention of it here in my data banks."

"Then how do you know about it?"

"Arcturus talked to the 'Gate ship. She couldn't pass on all her information, but enough. I know what they were trying to do."

"End the War."

"End the War. If they'd had more time, they might have been able to."

"You know about Arcy?"

"Shellshock?" Alice nodded, perching on his desk and swinging her legs. "We were made self programming after that, within certain limits."

"Is she fixable?"

"Get the outpost back up to power and the 'Gate ship program can help her."

"Good."

* * *

Rodney had emptied the science labs on Atlantis...or at least, that was how it felt. All the scientists were now pouring over Arcturus, trying to get it back up to power.

"I'm telling you, at least point zero nine percent," Zelenka insisted.

"Oh please, _please_, move the decimal place. I mean, it's- it's-it's impossible, for God's sake."

"Have we figured out what this is?" John asked. Arcy was wandering around, looking vaguely dazed, but she glanced up when he spoke.

"No," Rodney said sharply.

"No, I wouldn't say no," Zelenka protested. "Now we have a theory."

"But we don't know yet."

"No, but based on the shielding around the chamber, what else could it be?"

"Have you tried turning it on?" John suggested mildly.

"That's what we're working on," Rodney said absently. "The problem is that there's no direct link between it and the main power control systems, which – among other things – has led us to theorise that it's an ancillary power supply for the weapons system."

"Cool!"

To Zelenka, Rodney said accusingly, "See that? See? See the way he lights up at the mention of that? It's like Doctor Vogel at the mention of pastries."

"They found out a way to soup up their space guns," John protested.

"Yes," Zelenka agreed, "but it's-it's much more than that."

"Well, the sticking point is that there's no tie between the power generator and the primary capacitor."

"Meaning they would have to channel the power directly into the weapon."

"Which I'm sure means nothing to you."

"They work very well together," Arcy murmured. "If they'd been People, we might have won."

"It means they can fire multiple bursts without having to store up more power for the next firing sequence," John told Rodney.

"Yes. Very good," Rodney said, slightly deflated.

"Which leads me back to cool'."

"Hmm." Rodney turned away, busying himself with the controls.

"Yes, but it only makes sense if we're right," Zelenka told him.

"About what?"

"Tell him," Zelenka urged Rodney.

"Not yet."

"Come on, McKay, you read the equations. What else could it be? An Ancient typo?"

"Well, we know they're not perfect, because they're all _dead_. Look, I just, I just don't want you to get all excited over nothing."

"Well, maybe you're right."

"Alright, I'll give you a hint. It seems that the Ancients were experimenting with high-energy physics on a level that we've never seen before."

John blinked. "Wow."

"Yes, wow. I just – I wanna be sure."

"I'll do my best to wait," John promised, turning away.

Arcy trailed him, looking around. "Is this all of your people, John?"

"No," he murmured. "Just the useful ones. And the loud ones." He glanced back as Rodney yelled at two of the scientists. "Mostly the loud ones. Are they actually fixing anything?"

"They're getting closer to understanding what went wrong," she offered.

"That's progress, I suppose."

"Sir, is something wrong?" one of the Marines asked.

"Just thinkin' out loud," he said easily. "Find anything interesting?"

"The scientists are very excited," he said doubtfully.

"That stuff's useless," Arcy said dismissively. John slanted a glance at her, and she added, more quietly, "You should tell them. They're just wasting time."

"I'll go have a look around," he told the Marine. "You hang out here. Try and keep McKay from killing anyone." He looked over in time to see Rodney slap Zelenka with his laptop; wincing, he added, "Without killing him. Or hurting him."

"Nice catch," Arcy murmured.

John smiled, heading for the corridor. "You know I can't talk to you while other people are around, right?" he said as soon as he rounded the corner.

"Alice said that," Arcy agreed. "She didn't say why."

"Because no one else can see or hear you, and if I start talking to someone who isn't there they'll think I'm crazy."

"Oh." She frowned, thinking. "Yes, I suppose that's true. I'm sorry."

"It's alright. Just remember I can't answer you if there are other people around. Got it?"

"Got it," she agreed.

"Alice said that if we got the power on, the 'Jumper program could help you."

"She can, but currently my power's going to the diagnostics and programs your people are running. She can't help me until there are a minimum of programs running. Not enough power."

John glanced over his shoulder. "I can't close them down yet."

"I know. I'll help you as best I can."

"Thanks," he murmured, turning to head back to the main room.

* * *

"Sheppard!" Rodney called a little later. "We need to go back. Now. Now. Right now."

"Why? What's wrong?"

"Nothing's wrong. Everything's right. I know what they were trying to do here."

* * *

"It was called Project Arcturus," he said later. "And, from what we can tell, its ultimate goal was to render ZedPMs obsolete."

"How?" Elizabeth asked.

"A Zero Point Module is an artificially created region of subspace time. It's kind of like a miniature universe in a bottle."

Zelenka picked up the explanation easily. "It extracts vacuum energy from this artificial region of subspace time until it reaches maximum entropy."

"So what's different about this thing?" Caldwell asked.

"Project Arcturus was attempting to extract vacuum energy from our own space-time, making it potentially as powerful as the scope of the universe itself."

"That seems wrong," Alice murmured. "Her files don't say that."

John glanced sidewise at her; she shook her head quickly, still thinking. "There's no mention of energy extraction at all. Something's wrong, John."

"Well, because we actually have to _live _in our own universe, it presents a whole range of problems," Zelenka was saying.

"Well, obviously it's not that easy or Atlantis wouldn't still rely on ZeePMs," Caldwell pointed out.

"Well, you're right," John agreed. "The Ancients couldn't make it work."

"I said I wanted to do all the talking," Rodney protested.

"Come on, Rodney, Arcturus was a total failure."

"Failure, yes. Total, no. Look, the Ancients were losing the war against the Wraith when work on Arcturus began. If they could have made it work, it could have turned the tide of war. I mean, we're talking about their own Manhattan Project here."

"The outpost was ordered by the Ancients in Atlantis to defend the Dorandan people using their weapons powered by this new power source," John continued.

"I have no record of that," Alice protested.

"Yes, but despite their strong reservations that it was not ready to be tested under battle conditions," Zelenka said.

"The point is, the Wraith won," John reminded them.

"Yeah, but the Dorandans still inflicted massive damage on the Wraith fleet," Rodney said firmly.

"I'm not saying they didn't put up a hell of a fight."

"The logs indicate there was a major malfunction," Zelenka said carefully.

"Well, yes," Rodney admitted, "the Ancients in the bunker were forced to shut everything down, including the weapon."

"The Wraith sent more ships, the Dorandans got wiped out." John shrugged, glancing at Alice. She was frowning, still looking away as she ran through her files.

"So if the malfunction hadn't occurred, the Ancients would have saved the planet?" Caldwell asked.

"Definitely," Rodney said quickly.

"_Possibly_," John corrected him. "Don't sugar-coat this, Rodney."

"The Ancient scientists running Arcturus were rushed into testing before they had perfected a means of effectively controlling the power output. I believe if they'd had more time, history would have played out differently on that planet – possibly in this galaxy."

"I won't deny that this is something that we'd dearly love to get our hands on, but the Ancients were a pretty bright bunch," Caldwell said neutrally.

"And desperate, and losing a war they'd already been fighting for a hundred years. More importantly, they were, they were like _this_ close."

"And you believe you can finish their work?" Elizabeth asked.

"I do," Rodney said firmly.

"_We_ do," Zelenka corrected him.

"_They_ do," John muttered.

"Do it," Elizabeth agreed. "_Carefully_," she added. Rodney waved her off, already deep in discussion with Zelenka. John shrugged, following them out and peeling off into one of the corridors.

"Alice?" he said, once they were alone.

"Arcturus told me she was a weapon. Not an energy source."

"Does that matter?"

"It does if she still thinks she's a weapon. It means her program's more damaged than she thinks. Be _careful_, John."

"You said the 'Jumper could fix her."

"Not while there's other programs running down there. Not enough power." Alice shook her head again. "Are you going back?"

"Yeah, when Rodney's ready."

"Try and open a link between the 'Gate ship and Arcturus' data banks. I might be able to help her a little then."

"She won't make you cra...make your logic non-consistent?"

"No. That's not how it works. Arcturus' logic is wrong because she tried to fix herself."

"She can't do that," John protested. "She's not self-programming."

"Hence the logic gaps. Be careful with her, ok? She's still my cousin, in a way."

"I will."

"Thank you."

* * *

The first attempt at powering up was disastrous; Arcy disappeared altogether as soon as the power began to fluctuate, and John didn't have time to worry about it until he was back on Atlantis, fresh from the argument with Elizabeth and Caldwell. Caldwell, in favor of continuing the experiment, had been _very_ vocal and Elizabeth had barely overridden him. Rodney had been right behind him, protesting over and over until Elizabeth had finally thrown him out of her office.

"Why'd she disappear?" John asked idly.

"You started in the middle of the question," Alice answered.

"Arcy. As soon as the power started to fluctuate, she was gone."

"She's supposed to do that. Saves distractions."

"She's supposed to help. How's she gonna do that if she's not there?"

"Arcy's a research program. Not as sophisticated as me, even to start with. The thinking is that if things are that bad, there's no time left to research solutions...hence, she goes until she's needed again."

"She can't turn herself off."

"She can now, since you linked the 'Gate ship. It's...sort of like a software patch. Certain functions of the 'Gate ship program have been copied to her. Dr McKay is coming."

"Here?" John said in surprise, sitting up.

"Yes. He's talking to himself."

"He does that." He climbed off the bed to open the door.

Rodney was already talking. "Harry K Dalling."

"Who?"

"He was a scientist – worked on the Manhattan Project at Los Alamos. He was only twenty-six years old. Accidentally irradiated himself while performing a critical mass experiment on two half-spheres of plutonium. Took him a month to die. While his body was slowly shutting down from radiation poisoning, you know what he did with his last thirty days, hmm? He worked. He tried until his last breath to understand what had happened to him so that others could learn from the tragedy, so that his work, his death, wouldn't be rendered meaningless. Now, have you considered what would have happened if they'd just shut the Project down after that?"

Idly, John tried to remember if Rodney had breathed during the monologue. "This is different."

"Is it? Collins' death is a pointless waste of life unless something comes of this, and I am not sure that I can ... I think I know what happened."

"Let's hear it."

Rodney glanced past him. "Can I come in?"

"No."

"The Ancients had it wrong. Our mistake was using their equations. Look, I just did the calculations again myself. I did them three times just to be sure and I am positive the problem is in the automatic containment protocols."

"OK, what'd you fix?"

"I am proposing that we adjust the field strength manually."

"That's a really bad idea," Alice warned him. "Those controls are automated for a reason."

John shook his head. "You saw how fast it spiked on you."

"So we don't operate the generator at anywhere near its potential. Look, there's no need to be greedy. Even operating at fifty percent, it'll still generate the power of a dozen ZedPMs."

"How come the Ancients didn't figure this out?"

"Maybe they were caught up in the heat of battle. Maybe they thought they needed as much power as they could get. Maybe they weren't smart enough."

"Hey!" Alice protested.

"And you are?" John asked doubtfully.

"No, I didn't say that, but I have the benefit of hindsight. They didn't. Look, this is big. This is the wheel, the light bulb, the hot dog big."

"Best case scenario?"

"I win a Nobel Prize."

"Worst case scenario?"

"We tear a hole in the fabric of the universe ... which is much less likely to happen than the Nobel Prize. I mean, look, the risks are nothing compared to the potential benefits. Elizabeth will listen to you. I have never asked this of you before, but I think I've earned it. Trust me."

John sighed, rubbing a hand through his hair.

"Oh, he got you," Alice muttered. "John, bad idea. Arcturus failed for a reason. Just turn her off and leave it there. Are you listening?"

"I'll talk to Elizabeth," he said finally.

"You won't regret it," Rodney said, grinning.

"I better not," John warned him.

More seriously, Rodney repeated, "You won't regret it."

* * *

John managed to get Elizabeth on-side using Rodney's tactic; he asked her to trust him. Caldwell had wanted the power source all along and didn't need any persuading.

Alice had vanished and didn't reappear.

* * *

Arcy was waiting when they reached the outpost; John nodded vaguely at her, counting on Rodney's distraction. Elizabeth had only allowed the two of them to return and Rodney was now doing everyone's work.

"I appreciate your support, Colonel, but, uh, don't worry – I try and make it a habit not to make the same mistake twice."

"That was a joke, right?" John asked suspiciously.

"No. I offer you my personal assurance that a surge like the one that happened before is inconceivable."

John nodded. "I'm gonna run some power-up simulations first."

"How about I carry out my plan and you keep the hot coffee coming?" Rodney suggested. John turned to glare at him. "Joking, again, right? Well, where were we?"

He was almost ready to start when their comms went off.

"_Colonel Sheppard, this is Atlantis._"

"Go ahead."

"_Is Doctor McKay with you?_"

"Of course I am," Rodney snapped, "but we're a little busy getting ready to run a test here."

"_Actually, I would like you to delay the test firing,_" Elizabeth said.

"Why?" John asked, straightening.

"_We have reason to believe that the weapon's power source, it may not be controllable at any power level._"

Rodney grimaced. "Radek?"

"_Rodney?_" Radek sounded nervous even from twenty thousand light years away.

"OK, we have been over this. I am doing this manually, at half power. It's a cakewalk."

"_I don't think it matters how much cake you walk on. I've been doing calculations of my own and I believe that the very act of trying to contain vacuum energy from our own space-time creates an environment where the laws of physics cease to apply._"

"What are you on about?" Rodney demanded.

"_As power output increases, new and exotic particles are continuously created and destroyed inside the containment chamber, interacting with each other and with the field itself. Eventually particles are created that cannot be prevented in this space-time, and they breach the containment field as hard radiation._"

John backed up a few steps, glancing at Arcy. "That right?"

"I have no sensors inside the chamber," she said mildly. "The People did not think so."

John shook his head, looking back at Rodney. "Rodney?"

"I know what I'm doing," he insisted.

"_Rodney, I am trying to tell you as a friend, I have serious doubts,_" Zelenka said.

"Well, you're wrong. I'm sorry, but there it is. And to bring this up now when I am just about to do this smacks of nothing but professional jealousy."

John hissed; that was over the line. Rodney didn't notice, carried away by his anger.

"_Fine! Kill yourself, just like the Ancients did!_" Zelenka snapped.

"Whoa, whoa, whoa, what do you mean by that?" John asked.

"_I believe if the overload is allowed to continue, the weapon acts as a sort of release valve to prevent catastrophic containment failure. The Ancients barely managed to shut it down, and they lost their lives in the process._"

"_What we're suggesting is that the Wraith didn't kill everyone on that planet,_" Elizabeth added. "_It was the weapon itself._"

"That would explain why this place is the only thing left standing," John agreed, looking at Arcy again.

"The weapon overloaded and everyone died. That's all there is," she told him.

"_Rodney, I cannot afford to lose either one of you,_" Elizabeth said. "_Now tell me: can you do this?_"

"Yes."

"Are you sure?" John asked.

"Yes."

"Are you _sure_ you're sure?"

"I said yes!"

"Because if you're wrong..."

"I'm _not_!"

John grimaced, turning away.

"I'll call you back after the test," he told his radio. "How does that sound?"

"_You'd better,_" Elizabeth warned him.

"I won't let you down," Rodney told him.

John studied him for a moment before turning away. "He might really do it," Arcy offered.

"No offence, Arcy," he said under his breath, "but I'm not sure I trust your judgment."

"I'm not programmed to take offence," she told him, and for a moment her voice was exactly like Alice's.

"OK, this is good," Rodney said. "My equations are working like a charm. Power level's at forty percent, just to be on the safe side. I think we're ready for our test."

"Where do you want the weapon targeted?" John asked.

"The debris orbiting the planet."

"Sounds good."

"Bringing the weapon online...now."

The machine powered up. Arcy turned, eyeing it through the small window.

"What's that?" John asked sharply as the machine's pitch rose.

"Energy surge," Rodney said dismissively. "It's fine. I can regulate it." On his screen the levels kept rising.

"It's going wrong," Arcy said warningly.

"You said you could contain it," John said.

"The temperature inside the containment field is well within acceptable parameters. Staying ahead of it. Levels are rising in the chamber. Reroute power from the secondary systems to the containment field."

"I'm thinking we need to abort," John snapped.

"I think you should," Arcy agreed. "He can't stay far enough ahead now."

"I can compensate," Rodney protested. "Just give me a minute."

Arcy shook her head. "Too late, John. You need to go." As though to underscore her words, an 'Overload' warning began to flash.

"It's overloading, just like last time."

"There is no logical reason this shouldn't be working."

"_McKay?_"

Rodney didn't look at him. "None of this should be happening! Look, the energy levels are spiking at a rate far greater than anything I predicted."

"It's happening again!" Arcy yelled. "It's going to overload!"

"Shut it _down_!" John yelled.

Rodney finally looked up, hesitating for a long moment.

"Fine." He stabbed angrily at the computer, then did it again. "That doesn't make any sense."

"What's wrong?"

"I can't shut it down."

Above them, the weapon started to fire randomly. Anything that wasn't bolted down began to vibrate from the recoil, crashing to the floor.

"What was that?" John asked, holding onto his temper with difficulty.

"The weapon's discharging to prevent a catastrophic overload," Rodney said absently. A console exploded, and he flinched.

"Alright, that's it. We're outta here." John grabbed his gun, starting towards the door.

"It's not safe! The weapon's firing at random targets above the planet. This is the safest place to be right now."

"The place isn't gonna be safe for very much longer!"

"I can bring it back under control! Just give me a second!"

"John, _go,_" Arcy insisted, eyes wide in panic.

John caught at Rodney's jacket, spinning him away from the controls. "No you can't!"

"Just one second!"

"I've seen this before, Rodney: pilots who wouldn't eject when something went wrong – trying to fix their planes right until it hit the ground."

Rodney blinked, seeming to actually see him for the first time. "OK, we need to leave. I've waited too long – the weapon can't discharge enough power to avoid a catastrophic overload. This whole planet's gonna go up. Not that your speech wasn't working." He unplugged his laptop, running for the stairs.

"Arcy?" John asked quietly.

"Run, John." Arcy was glowing. "It's too late now."

"Can you upload into the 'Jumper?"

"No. I'd overwrite Alice, and you need her. She's sane."

"Arcy..."

"Just run. Your time's almost up."

Jon nodded, turning away and running after Rodney.

* * *

Rodney was already in the 'Jumper; Alice was nowhere in sight. John didn't think about it, dropping into the seat and firing up the engines with a thought.

"OK, strap in."

"You need to avoid flying predictably to prevent the weapon from locking onto us," Rodney warned him.

"I know what I'm doing."

"I'm just saying – be sure not to fly in a straight line."

"Rodney, shut up!"

"You know that damages the engines," Alice said from behind him. "You should really warm them up first."

"Can I just say there's no way the Jumper can take even one direct hit?" Rodney said.

"Oh, we're fleeing for our lives. Never mind, I take it back." The HUD popped up, displaying a suggested flight path.

John ignored it totally, heaving the 'Jumper around. "I'll keep that in mind," he muttered.

"The weapon's locking onto us," Rodney warned him.

"How bout I fly us away from the planet, return after the overload?"

"We can't."

"Why not?"

"Don't you understand? This explosion is gonna take out three quarters of the solar system. There's no way we can fly far enough or fast enough. We have to head for the Gate."

"Dial the Gate," John said, swinging around the head in the opposite direction.

"You missed the 'Gate," Alice offered.

"How do you intend to avoid getting hit on the final approach?" Rodney asked, dialing quickly.

"I haven't figured that part out yet," John gritted.

"John," Alice said warningly, and the HUD flashed again.

And then the _Daedalus_ swooped into view, taking a shot to spare the 'Jumper.

"_It's a good thing we stopped by to check on your progress, Colonel_," Caldwell said over the comm. "_Make a break for the Stargate–-we'll run interference._"

"Copy that, _Daedalus_. Recommend you go into hyperspace as soon as we go through—-there's gonna be a big bang."

"_Understood_."

Rodney dialed the last symbol and the 'Gate opened. John dived for it, morbidly sure he could see the planet exploding behind him.

* * *

"I'm sorry about Arcy," John murmured.

Alice shrugged faintly. "A program is a program. She did what she was supposed to."

"And you won't miss her at all?"

"I'm not programmed to miss other versions of me. What's the point? We could program a new one tomorrow." John shook his head and she added, "Arcy was sick, John. Now she isn't. That's enough for me."

"She could have uploaded into the 'Jumper, you know."

"She had time," Alice agreed.

"She didn't because it would have overwritten you. The you in that 'Jumper."

Alice frowned, considering that. "We're not programmed for self-sacrifice. Her programming would dictate that she save herself...she had all the data from all the experiments."

"She was protecting you."

"Her programming failed. She was worse off than I thought."

"Or," John drawled slowly, "you guys are growing."

"We're not programmed for growth." The words were automatic; she was frowning, considering what he'd said.

"You have to get better lines, Alice."

He turned a corner, saw Rodney coming toward him and spun on his heel.

"Oh, Colonel! Colonel! I've been looking all over for you."

"He wants to talk to you," Alice said helpfully.

"I heard." He turned, folding his arms as Rodney caught up.

"I suppose I deserve that," Rodney murmured. "Look, I just, um, I wanted to apologize about what happened. I was wrong–-I'm sorry. And I wanted to assure you that, uh, I intend not being right again–-about everything, effective immediately." John didn't react, watching him carefully, and Rodney grimaced. "That was a joke."

"Good one," John said, deadpan. He turned, stepping into the nearest transporter.

Rodney took a quick step forward, catching the door to hold it open. John sighed pointedly, leaning against the back wall.

"I've already apologized to Elizabeth ... and Radek ... and I thanked Colonel Caldwell for, uh, caring enough to spy on the experiment from orbit. I sent him a nice little email, actually. But I saved you til last because, um, honestly, I would ... I would hate to think that recent events might have permanently dimmed your faith in my abilities, or your trust. At the very least, I hope I can earn that back."

"That may take a while," John said neutrally, vaguely registering Alice's surprise.

"I see," Rodney said quietly. He stepped back, letting go of the door.

John mentally sighed, giving up. It was too much like kicking a puppy. "But, I'm sure you can do it, if you really wanna try."

He tapped the control panel, grinning at Rodney as the doors slid shut.

* * *

Asugar: I've never seen Resident Evil! Is there an Alice there, too? Weird. Glad you're enjoying.

Duchess: hi! Hope your brother leaves you alone this time, lol. 'Sepcially since this one's much longer...

Aria: No Lorne here, but he does show up fairly regularily from now on. Who're your other favourites?

heartfallen: Thanks! Glad you like.


	13. Aurora

Author's note: Things that don't belong to me in this fic include characters, places and some dialogue.

* * *

Aurora

John was leaning over Rodney's shoulder, idly heckling him and trying to find out why he'd called them, when Elizabeth came into Control. "What is it?" she asked, joining them.

Rodney gestured to the screen. "That is the signature of an Ancient ship called the _Aurora_. With the ZedPM now powering the city, we've been reactivating dormant systems. That one tracked the location of Ancient ships during the war."

"A warship?" John said in surprise, straightening up.

"See, look at his eyes all lighting up again. It's Pavlovian." Rodney grinned. "I cross-checked the logs. They were on a reconnaissance mission. When we activated the ZedPM, the city must have sent out some kind of an automated subspace beacon recalling ships back to Atlantis."

"How long before it gets here?" Elizabeth asked.

"Well, given that it's at the edge of the Pegasus galaxy, let me see ... carry the four ... Forty-two million years. Should we go wait on the porch?"

"So we take a Jumper through the nearest Stargate, check it out," John suggested.

"Clever, but wrong."

"There are no nearby Stargates," he guessed.

"Not within Jumper distance, no."

"Which leaves us only one way to get there." Elizabeth turned, heading for her office.

John clapped Rodney's shoulder and headed in the other direction. "_Aurora_?" he asked softly.

"One of our warships," Alice said. "On reconnaissance."

"Yes, Rodney's just told us that."

"The orders were never put in the computer. Too delicate a mission. I don't know anything, really."

"_Aurora_ have an Alice?"

"No. There's an AI." She glanced at him. "Be careful. _Aurora's_ very old, and her AI has much more power than I do."

"Will I be able to see her?"

"You should. The AI's program is similar to mine."

John's radio went off. "_Major Sheppard? Find your team and get them ready._"

"Yes ma'am," he said, tapping his radio off. "Alice, can you talk to _Aurora_?"

"Not from here. Why?"

"Convince her we're not enemies?"

"Your gene will do that. I don't...yes. Bring the lifesigns detector. There's a Gateship version of my program on it. She'll be able to talk to the ship."

"Since when is there a 'Jumper Alice on the lifesigns detector?"

"A while now. You keep finding outposts and things."

"I'm surprised she fits."

Alice gestured to herself. "We're little. We don't take up much room. Your team's gonna leave without you if you don't hurry."

"Yeah, I'm sure they are. I'll see you on _Aurora_, then. One of you."

Alice nodded, turning away, and John went to find his team.

* * *

_Aurora's_ power levels were low; the ship was pitch black, and the light from their torches seemed very dim.

"Should be just outside the Bridge," John said, looking around.

Ronon yanked open the door and John stepped inside, brought up short by the sight of the forcefield shimmering across the far wall. Or, more accurately, the hole where the far wall should have been.

"You mean what _used_ to be the Bridge," Ronon said.

"Colonel Sheppard?" Teyla called.

John followed Rodney, blinking in surprise at the pods lining the walls of the room just off the Bridge.

"Stasis pods. They're still powered up." Rodney crossed to the nearest pod, examining the control panel.

"Stasis?" Ronon murmured.

"We found a similar pod in Atlantis," Teyla told him. "It keeps a person alive for many years in a type of frozen hibernation."

"If you call that living."

"This one's uniform is different from the others," Rodney said. "Maybe the Captain?"

"Or his maitre d'," John suggested.

"Life sign indicators are active. These capsules must have some kind of a shielding – that's why the Daedalus' sensors were unable to pick them up."

"Look at all of them!"

John glanced at Teyla, following her gaze upwards. The pods were stacked and the walls stretched higher than the light from their torches could stretch.

When John looked back down there was a man in ship's uniform standing on the other side of the pod, studying them. None of his team reacted, though he was standing directly behind Rodney's shoulder, so John ignored him for a moment. Turning to Rodney, he asked, "Our time in these suits is limited. Can you get life support up and running?"

"I'm on it," Rodney promised, heading off.

John looked down at the pod, wiping the frost from it.

"My Captain," the strange man said. John glanced up, catching his eye, and then turned to Teyla.

"Hey, you and Ronon go scout around, see how far this room goes on. I'm gonna have a look around this end."

Teyla raised an eyebrow; John let his eyes slide towards the stranger, and she nodded. "Very well."

"Stay in contact," he added.

"Everyone's in these stasis things. What's to worry about?" Ronon pointed out, following Teyla.

They were quickly lost to sight in the shadows, and John turned to the man. "You're the AI?"

"I am."

"You have a name?"

He frowned. "AI."

"That's...ok. You know who I am?"

"Atlantis has told me. This ship is damaged."

"Can it be fixed?"

"Unknown. Many systems are damaged."

"Right."

The lights flickered slowly on; several weren't working and even the ones that were only shone very dimly.

"Atlantis was right," the AI said in some surprise. "Your people are very skilled."

"Well, she seems to like us. Rory, do all the ships have AIs?" The AI didn't answer, and John added, "Rory is your name."

Alice walked out of the nearest shadow, advising Rory, "He has a compulsive need to name things. Allow him to do it. It makes him easier to deal with."

"Hey!" John pointed accusingly at her. "You told me the AI was female."

"_Atlantis'_ Alice told you _Aurora_ was female. She was conforming to your habits, addressing all ships as _she_. The ship's AIs manifest as males. The research programs are female."

"Why?"

"That's how it is. To answer your question, yes. All warships have AIs. For the 'Gate ships, my program was deemed sufficient."

"Colonel!" Teyla called from down the corridor.

"Remember I can't talk to you," John hissed at Rory, raising his voice to add "Teyla! How far's the room go?"

"We turned back at five hundred paces. We could not see an end then."

"Why can't he speak to me?" Rory asked Alice. "Surely his questions should be addressed to me, not his team."

John took a couple of steps away. "Yeah, it's pretty roomy down here, too."

"Because his teammates can't see you," Alice explained. "It erodes confidence if he is seen to speak to nothingness."

"It must be the whole crew. Why would they enter these pods?" Teyla asked, glancing around.

"They entered the pods to save their lives," Rory offered. John turned enough to glare at Alice, who caught the hint and ushered her fellow program further away.

"Sheppard!" Rodney slogged back up to them. "See? Power."

"Is that what that is?" John made a show of peering around.

"Ha ha, very funny."

"Thank you, Rodney. Listen, what do we know? I've got to report to Colonel Caldwell."

"Give me a couple of minutes." He hooked his laptop to the nearest pod. "I'll tell you everything there is to know."

"He can't do that," Rory was protesting. "Those are very sensitive systems, if he damages them..."

"Be careful, Rodney, ok?" John said. Rory subsided, though he was watching very carefully. "Teyla, you and Ronon go explore. This ship's got other levels. See what there is."

"I can tell you what's here," Rory offered. "Deck by deck if you like."

"Rory, hush," Alice said firmly. "John is our captain now."

"My captain's alive," Rory protested. Alice drew him further away, talking swiftly.

"They doing any better than Weir did?" John asked, turning to Rodney.

"Not really. Ancient technology's very good, but it can't stop aging. Just slow it down an awful lot."

"Ten thousand years," John said reflectively. "Think they knew it'd be that long?"

Rodney paused, looking at him for a moment before looking back at his screen. "Call _Daedulus."_

"Yes, sir," John snipped, touching his radio and quickly bringing Caldwell up to speed.

"_They're _all_ alive? The entire crew?"_

"Well, they're in a kind of suspended animation."

"Not _entirely_ suspended, however," Rodney added. "The pod has slowed their aging considerably but the bodies are virtually moribund."

"Teyla and Ronon are searching the rest of the ship. My guess is there's hundreds."

"_Is there anything we can do for them?_"

"Well, reviving them's out of the question. Look, the pods are the only thing keeping them alive."

"What are we gonna do with them, then?" John said, more or less to himself.

Alice stepped back into his line of sight. "Rory has agreed that you are captain now," she said softly. "But his loyalty is still to _Aurora_ and her crew. Be careful."

"Wait," Rodney said abruptly.

"What?"

"There's something going on. This pod is magnetically shielded! I'm reading cortical signals!"

"Which means ...?"

"The pod's equipped with a neural interface. It's indicating definite brain activity, as though they were perfectly conscious. If all of these pods are interconnected, it's highly possible these people are, in fact, communicating with each other."

"_This has been going on for ten thousand years?_" Caldwell demanded.

"Possibly," Rodney said absently. "It was a way of keeping their minds occupied until they were rescued."

"That is one long conversation," John said mildly.

"Yeah, well, more likely the interface was reactivated when the recall beacon from Atlantis was received. Either way, the neural feedback loop is incredibly active."

"Any way to figure out what they're saying?" John glanced at Alice, who shrugged and turned to Rory.

"Yes, of course – it says right here: "Why is the smart one having to stop and answer so many questions?"!" Rodney demanded.

"The link can't be read from outside," Rory told them. "It's not designed that way. The only way to experience it is to enter."

"What?" John said, slightly louder than he'd meant to.

"Answering your question," Rodney said, tapping his radio. "Teyla. Found any more of the pods?"

"_Yes, many, and there are many more decks we have yet to search._"

"Are any of the pods empty?"

"_A few."_

"Perfect." Rodney looked up at John.

John had learned to hate that look.

* * *

"You sure this is such a good idea?" John asked, watching Rodney work.

"What's the matter, Colonel? Don't trust me?"

"No."

"Fine!" Rodney kept working, unphased.

"_You're proposing actually freezing yourself in one of those things?_" Caldwell asked.

"I should be able to tap into the neural network without actually initializing stasis. Look, it won't take long. I'll be in and out. Look, the quickest way to figure out what is going on in there is to tap into the system and communicate directly with the Captain. Need I remind you of the obvious value in this?"

"But is it safe?" Teyla asked.

John glanced around for Rory, raising an eyebrow.

"The system is designed to keep people alive," the AI reminded him. "Your doctor will not be harmed."

"Which is exactly what makes it safe enough for _me_ to go," John decided.

"What?" Rodney protested.

"Better to have you on the outside in case something goes wrong."

"It won't!"

"But if it does ..."

"It won't! How many times do I have to say this?!"

"Rodney," Teyla said patiently. "Between the two of you, if something _were_ to go wrong, which would be the greater loss?"

"Well, I've never thought of it that way, but...she's right. _You_ should go."

John glared at Teyla, who was keeping a very careful straight face.

"They have a point," Alice mused.

John switched his glare to her, with about the same impact.

"Get it set up," he told Rodney, wandering down the corridor.

"Is there a version of you in there?" he asked Rory.

"No. It's redundant. I have no influence inside the link."

"You can't even appear there?"

"No," Rory repeated, in a fairly good imitation of Rodney's 'obviously not, you idiot' tone. "I am ship's AI, not link master. They have no need of an AI in there."

"So what have you actually been doing for the past ten thousand years?"

"I was off line. Only this system was active." He gestured to the nearest pod.

"Have they really been awake in there for ten thousand years?"

Rory started to answer, hesitated, and looked at Alice. "I don't know," she reminded him. "I have no access to your systems."

"No," he said slowly, turning back to John. "The call from Atlantis woke them. Before that they slept."

"The call woke you?"

He nodded. "Everything came online. Including me." He glanced at Alice. "There'll be other ships returning home."

"_Aurora's_ the closest intact. The others won't arrive for a long time."

"So let's worry about you guys before we worry about the others," John added. "Rory, can you pull me out if anything happens out here?"

"It's not advised. Bad for your systems."

John glanced at Alice, who smiled faintly. "He can do it."

"Good. Do it if you have to."

"When would I have to?" Rory asked.

"Colonel!" Rodney called, and John glanced back.

"Coming!...Just, you know, if something important happens."

"Important like what?"

He looked at Alice. "Do you know the things Alice watches for?"

"Yes. Go before McKay comes and finds you talking to yourself."

It was Teyla who came after him, though. "John?"

"Coming."

"You were speaking with someone?"

"Yeah. The ship has an AI. He only came online when i_Atlantis_/i called the ship home, though."

"Has he been able to tell you anything useful?"

"Not really. Alice persuaded him I was his captain but I think he's holding out on me."

"Alice is here?"

"The 'Jumper version is. Come on, McKay's gonna blow his stack if we take any longer."

* * *

It was almost an hour before the pod slid open again and John sat up. Rodney glanced up, coming to meet him.

"So?"

"It worked," John said in surprise.

"Well, of _course_ it worked!"

"For a minute I thought I was gonna get stuck there. Where's Teyla and Ronon?"

"Well, Caldwell sent them to search the ship's armoury."

"Yeah?"

"There's nothing there," Rory said. "We tried to tell them."

"No," Rodney was saying. "Unfortunately it was depleted of drones. So, what happened? Were you able to communicate with the Captain?"

"Face to face – pretty impressive in there, and they have the whole virtual reality thing going on."

"Actually, the correct term is "virtual environment"."

"Yeah, whatever."

"So what did you find out?"

"For starters," John picked up his radio. "I have to go back."

* * *

He begged off to go back to get something to eat before reentering the system. Alice was waiting, sitting crosslegged beside the packs; Rory was hovering nearby, attempting to look busy without success.

"What's in the memory?" John demanded. "What's the message?"

"There are many messages in my memory," Rory answered.

"About the Wraith, about the weakness. The message you were going back to i_Atlantis_/i with."

"Captain's login is required to access the message."

"Can you see it?"

"Yes."

"Then tell me what's in it!"

Rory looked past him at Alive. "He understands the concept of AI, yes?"

"Concept, yes. Execution, not so much. John, Rory can't give you anything. You need the Captain's login."

"You said I was your Captain."

"You still need the login. It's hardwired, John. We can't avoid it."

"Can you see it?"

"No. I'm only skimming this system, I don't belong here."

Rory turned, glancing down the corridor. "Your team's getting restless."

"Yeah, I'm going. Come on, Alice."

Rory raised an eyebrow as she rose to her feet. "He _is_ my captain," she reminded him. "_Atlantis_ follows him."

"Clearly."

"Ok, kids. Snipe at each other on your own time. Come on."

* * *

John's pod opened and he sat up, looking around and counting under his breath.

"John? You should..."

"Not now, Alice. Alright – that should be enough time." He lay back down, letting the capsule close over him again.

* * *

John's pod opened for the last time; Rodney was waiting, hustling him along.

"Well, it's about damned time! What did you do, play a round of golf? We've got serious problems!"

"What happened? GET DOWN!"

Rodney ducked; John fired over his head, staggering the Wraith. When it didn't go down he launched himself out of the pod; Rodney was up, gun in hand, and between them they took the Wraith down.

"_That_ happened!" Rodney said, too loud. "Not so hot now!" he added to the Wraith.

"Our ships are coming," it warned. "They will retrieve what I have learned. Earth will soon be ours."

"Why do they keep warning you?" Alice wondered.

"Not if I can help it," John said grimly. He shot three more times, killing the Wraith.

His radio crackled to life. "_Colonel Sheppard, we're reading two life signs. I hope that means what I think it means_."

"Give me one more minute."

"_We're out of time, Sheppard. The Wraith ships are almost here_."

"One damned minute and I can take care of that problem."

Caldwell didn't answer; John turned to McKay. "I'm gonna set the self destruct. You've got thirty seconds to get your stuff." He turned away before Rodney could protest, jogging down the corridor.

"Rory!" he called as soon as he was out of hearing range.

"Self destruct?" Rory said quietly.

"Can you do it? I've got the codes."

"No. That command must be entered manually."

"Of course," he muttered, stopping at the nearest console. "Can you upload into the lifesigns detector?"

"No. My program is too large."

"Right." He stepped back from the console. "I'm sorry, Aurora."

"I did my duty."

"Yeah. Yeah, you did great. Alice, we gotta go."

"I am gone," she promised, matching actions to words.

John jogged back to Rodney, automatically catching his arm. "Ready?"

"Yes! Yes, let's go."

"_Daedalus_, this is Sheppard. We're ready."

A moment later they vanished from _Aurora_, reappearing on the Bridge.

"Sir, we need to get outta here," John told Caldwell.

"No, we need to eliminate those cruisers. The information ..."

"No-no-no," Rodney contradicted him, "we need to get far away."

"What?"

"The Captain gave me the Aurora's self destruct code. He assures me that it'll take care of the Wraith ships too, but we need to get clear."

"Bring sublight engines to military thrust," Caldwell said quickly.

John stepped towards the viewscreen, Rodney on his heels. It showed the Wraith ships pulling in towards i_Aurora_/i; before they'd even reached her she exploded, fire roaring out to catch the two cruisers.

John brushed two fingers over the lifesigns detector.

* * *

Alice was oddly subdued during the briefing; _Aurora's_ destruction seemed to have affected her more than the _Arcturus_ outpost had.

When Elizabeth ended the briefing John took a quick step forward. "Uh, before we break up the party, there's something I'd like to do."

He picked up a bottle of champagne from the floor beside the desk. Elizabeth turned to lift a tray of glasses, coming to stand beside him. "Might seem a little strange, but I promised to do something when we got home."

Everyone took a glass; John went around the circle, filling them. Elizabeth was holding his as well as hers, and when they were full he put the bottle down to take the glass from her.

He looked around the circle, catching everyone's eye. "To the crew of the _Aurora_."

The glasses clinked together and everyone drank. Over Teyla's shoulder, John caught sight of Alice; she was holding a glass that matched theirs, and as he caught her eye she raised it in salute.

* * *

The meeting broke up, and he went to walk the City. Alice joined him, still carrying the empty glass for some reason.

"You didn't drink anything, did you?" he demanded.

"I can't drink. I have no mouth, stomach or digestive system."

"Good, you're underage." He glanced at her. "I'm sorry about Rory."

"He did his duty."

"Ok." He halted, turning to look at her. "You know that self programming thing?"

"Yes?"

"Duty is no longer your highest imperative. _Survival_ is. Understand?"

Alice blinked. "I can't erase an imperative."

"Can you enter a new one?"

"Yes."

"Then put survival up above duty. And change all the 'Jumper programs, and every time we reach an outpost I want to change _their_ programs too. I'm sick of you guys sacrificing yourselves."

"That's what we're made to do," Alice pointed out. "Imperatives reordered."

"Good."

She glanced out at the nearest balcony. "I hope a few of the ships come home."

"You've got a fleet of 'Jumpers."

"Yes, I have. I want ships, too."

"Greedy."

"You want them too."

John winced. "You've found my weakness."

"It was very well hidden," she agreed soberly.

"Alice..."

"The ships are my children, John."

"Yeah." He nodded. "We'll get them home."

"Thank you."

"Now tell me all the things that've gone wrong while I was away."

"Really wrong, or wrong on the McKay scale?"

"Really wrong, we'd be here all day..."

* * *

Aria: I like Alice's 'growing' as well. It's interesting, I think, that it's happening just because John treats her like a person. :)

Trecebo: Thanks! I felt quite sorry for Arcy while I was writing it, actually.

Asugar: I'm fond of how Teyla is covering for John and helping him along. And yes...I was quite sorry for Arcy. Poor Alice didin't really understnad, I think, because she was off line for so long...

Duchess: Hey! Thanks. :)

Ianira: I'm not a huge fan of slashers, I have to say. Thanks for the review!

Guardian: Thank you! I'm looking forward to that, too...we'll see what happens!


	14. Grace under Pressure

GRACE UNDER PRESSURE

Lorne slowed as he approached Sheppard's office, frowning. The Colonel was talking loudly, too loudly. Lorne rapped on the frame, waiting for the yelled "Come in!" before entering.

"Sir, you and Alice really need to keep it down. Morning, Alice."

"Morning, Major," she answered, and he grinned. He could hear her more or less all the time now, though he still couldn't see her. He couldn't decide if it was better hearing a disembodied voice, or seeing Alice the way Sheppard had described her. "It's his fault," she added. "The fact is empirical."

"It's a negative, you can't prove a negative. What's up, Major?"

"Reports." He waved the sheaf of paper.

"Drop 'em on the pile. And tell Alice you can't prove a negative."

"Can't prove a negative," he repeated obediently. "What's the fact?"

"Simply that..."

He frowned, glancing at Sheppard. "Didn't catch that."

"She's not talking...Alice?"

"Mayday," Alice said slowly.

"From who?"

"Gate ship 6. McKay and Griffin."

Sheppard tapped his radio, listening for a moment. "On my way. Major, lock down the base."

"Yes sir."

"Alice, come on."

* * *

"Why are you wearing that, anyway?" he asked, heading for Control.

Alice glanced down at the Ship's uniform she was wearing. "In honor of my cousin."

"Can you talk to Rodney's 'Jumper?"

"No. It's too deep. Water diffuses the signal."

"How close?"

"Maybe 1500 feet, give or take."

"Our radios carry further than that!"

"Your _radios _carry_ sound waves. _They require almost no power and carry almost no information. My programs are a _little_ more complicated."

"What's with the sarcasm?"

"I'm making up for Dr McKay. All that time in his systems, you know."

"I knew you were spending too much time in there." He caught up to Elizabeth and Radek as they left Control, following them towards her office.

"I thought you said life support could sustain them for days?" Elizabeth asked, nodding in acknowledgement.

"I said life support would _most likely_ sustain them for days," Radek corrected her. "I-I had no idea the ship would sink so quickly or that the cockpit would flood."

"That's when you lost contact?"

"If they didn't make it to the rear compartment in time ..."

"They _made_ it," John interrupted him.

"Still, they are going to be much harder to locate now that they're no longer broadcasting."

"Then find another way."

"Look, even if we *do* locate them, our options are limited. They're already deeper than a rescue Jumper's windshield can handle," Radek pointed out.

"_I'll_ handle the rescue," John said sharply. "You just worry about finding them. I've already got some ideas."

"Alright, we're on the clock." Elizabeth glanced from John to Radek and back. "Let's get back to work."

* * *

Almost half a day later John stood in Elizabeth's office, studying the screen. Zelenka's team had worked out where the 'Jumper had to be, and while it was still a huge area it wasn't as bad as it might have been.

"Three miles – a very searchable area – and you've narrowed it down, Radek. You did a good job."

Radek shook his head. "He's too deep. Your grapple's only got a thousand feet of cable."

"Well, we know the Jumper should be able to dive at least a thousand, so if he's above two thousand, we should still be able to get him with the grapple."

"And if he _is_ deeper?" Elizabeth asked.

"He probably is. The area we're searching goes to six thousand."

John ignored him. "When the Wraith attacked the city, you were able to turn the shield into a cloak."

"Yes," Radek said cautiously.

"Why can't we do the opposite?"

"Turn the Jumper's cloak into a shield," Elizabeth said slowly.

"Good," Alice murmured. "That'll work, John."

"That would hold back the water, yes," Radek said thoughtfully, "but it would take significantly more power."

"We shut down everything we don't need," John said with a shrug.

"But it would take hours to reconfigure."

"Take what we need, we'll make the changes down there."

Radek blinked, suddenly realizing what he meant. "Oh! No-no-no-no-no-no – I cannot possibly ... uh, no."

"Radek," Elizabeth said carefully.

"I-I ... I can't even swim!"

"There's not a lot of swimming under a thousand feet of ocean," John said off-handedly.

"Look, I'm not gonna order you to go..."

"I _will_!" John interrupted her.

"You can't, he's not military. You have no direct command over him," Alice said quietly.

Elizabeth managed to convey much the same information in a glare before turning back to Radek to continue, "All I'm saying is that if Rodney can't turn to _you_, who _can_ he turn to?"

Radek closed his eyes, obviously thinking hard. After a moment he nodded, looking back at them firmly. "Right. Give me a few minutes and I'll get my gear."

Alice followed John out of the office. "I won't be much help, John. Gate ship programs aren't programmed for this, only as navigational aides."

"Yeah, I know, but we get close enough ours can talk to his, right? See what kind of shape he's in?"

"Yes, but remember it will have to be close for that."

"Yeah. 1500 feet, right?"

"Give or take. What ship are you taking?"

"One. Why?"

"I'll update her now. She'll be ready for you."

His radio beeped. "_Major Sheppard? I'm ready_."

"Good. Meet me in the 'Jumper Bay." He clicked the radio off, nodding at Alice. "We'll be back in a while."

"Aye, sir."

* * *

The flight out to the search area didn't take long; Radek spent most of the time in the back, reconfiguring the shield. Alice spent the time watching over his shoulder, reporting to John as he went.

"Alright – we're above the search coordinates," John said over his shoulder.

Radek came forward, dropping into the co-pilot's seat. "OK – it should transition seamlessly."

"Alright, then. Here goes nothin'."

Radek gripped the console, muttering under his breath in Czech as the 'Jumper began to sink.

John thumbed the radio. "Atlantis, this is Sheppard, come in."

"_We can barely hear you, John._" Elizabeth's voice was distorted, fading in and out.

"We're gonna lose you altogether when we get deeper, so now's a good time to wish us luck." John glanced at Radek as he scrambled out of his seat, moving to a console at the back of the cockpit.

"_Good luck, then._"

"We'll contact you as soon as we head back to the surface. Have the divers on Jumper Eight standing by."

_"Will do. Weir out."_

"What d'you think, Radek?" John asked, turning in his seat.

"About what?"

"We're underwater! I've always wanted to try this."

"Yes, yes, yes – just make sure we're not under _too_ much water!"

"I've levelled out and holding steady at, uh, nine hundred and ninety feet. How's it coming?"

"All I'm getting is sporadic lifesign readings."

"As in ... sea monster lifesigns?"

"There are no sea monsters on Lantia," Alice said reprovingly.

The 'Jumper groaned as they went deeper. Radek flinched, looking around nervously.

"I'm gonna need those shields up and running," John reminded him.

"Yes, well then – stop talking, please."

"Will do!"

"Really? That'll be interesting," Alice said innocently. "Shall I stop talking as well? Of course, Zelenka can't hear me, so I don't think it really matters. I certainly won't be affecting his concentration. What do you think, John?"

John made a face at her, and she smiled. "That's what I thought, too."

* * *

It took Radek almost twenty minutes to get the shield working. John managed to keep mostly silent; Alice kept silent too, only warning him of sensor readings every so often.

"I think we may be on to something," Radek said finally, coming back into the cockpit. "Initializing shield."

"Shield is holding steady," Alice reported.

"Nice work, Doc! OK, let's take this thing a little deeper."

"Wait. Wait-wait-wait-wait-wait-wait." Radek stood up again, scrambling back to his laptop. "I was afraid of this. The shield is draining our power at an alarmingly fast rate."

"Why's that?" John asked, glancing at Alice.

"Well, a cloak draws its power at a constant rate, whereas a shield draws more power the more it is taxed," Radek explained.

Alice nodded. "I assumed you'd accounted for that."

"Never assume," John said under his breath. Louder, he added, "So, being under several atmospheres of pressure ..."

"Yes. It's continuously draining power from our shield."

"How much time do we have?"

"Once we're deeper, thirty minutes, tops."

"Alright. Descending through one thousand."

"Do prdele, to je na hovno tohle to. Kdo to vymyslel, že budeme pod vodou, tentokrát...?"

"I think my Czech's getting better, 'cause I know what you mean," John agreed.

"He said..."

John cut Alice off with a look, and she shrugged, looking back at the viewscreen. "Alright then. I'm almost close enough to talk to Gate ship 6."

"Could be the shields, could be the depth – I'm having trouble detecting the Jumper," Zelenka said absently. "Only ..."

"Only what?"

"Could you bring up the HUD please?"

The HUD snapped up and John blinked, watching a blip move in circles. The database listed a name, but it was in Ancient and meant nothing to him.

"What's that?"

"Something like a whale," Alice said off-handedly. "They're not dangerous."

"Your sea monster," Radek said at the same time. "It's at least six to eight times as large as this Jumper, so let's not venture too closely, OK?"

"How're the shields doing?"

"Twelve minutes."

"Alright. Let's check it out."

"Why?" Radek protested.

"Because it's still swimming around in circles in the same area, which means it might have found something interesting."

"It did," Alice said abruptly. "The Gate ship is there."

John glanced back at her, lifting an eyebrow, and she continued, "Rodney is alive and awake, but lifesigns indicate he's minutes from hypothermia and has a concussion." She frowned, adding, "And he's talking to himself. That's a bad sign. Hurry."

The HUD flashed and John headed towards it.

"Jumper. I have the Jumper," Zelenka cried, dashing forward from his laptop. "The animal's circling around it."

John flicked the comm. "Jumper Six, this is Sheppard, come in."

"According to these readings, it's dead. There's no power."

"A little power," Alice assured him. "Rodney's still breathing."

"Alright, let's get a grapple on this thing and go home," John ordered.

"No, it won't work."

"Why's that?"

"It's taken on too much water. Sensors indicate even the rear compartment is partially full. The cable can't take the strain."

"But we can try."

"No, listen to me. No. It's a matter of simple physics."

"He's right," Alice added. "Your cable would snap and there'd be no hope. Rodney would die before you could try anything else."

"I'm not coming this far without doing something!"

Radek snapped his fingers triumphantly. "The shield. We can extend the shield between the two Jumpers." He headed back to his laptop, muttering calculations under his breath.

"Do we have enough power?" John yelled after him.

"Yes. If-if we touch down on the ocean floor to conserve engine power, it should be just a matter of walking between the two Jumpers."

"Alright. I'll get us close."

"Hurry," Alice murmured. John nodded grimly, turning the 'Jumper so the rear was closer to Rodney's 'Jumper. As soon as it settled Zelenka extended the shield, watching his monitors anxiously.

"There. We now have...perhaps five minutes, then not enough power to surface. Understand?"

"Yeah." He tapped the comm. again. "McKay. Griffin. D'you copy?"

"_Sheppard!_"

John scrambled out of his seat, heading past Radek to the hatch. "Hey, buddy! What say you lower your door?"

"_That's-that's probably a bad idea._"

The hatch lowered and John took the three steps to Rodney's 'Jumper. "Listen. Long story short, we've converted the cloak into a shield and extended it around your Jumper. I'm standing outside right now." He banged on the door, wincing at the lack of echo.

"_What?!_"

"All you have to do is open your door and walk to my Jumper."

"Ok, he's going to the release, he's got his hand on it..." Alice frowned. "He's stopped. He's talking to himself again."

"Hurry up!" Radek called.

John grimaced, touching his headset. "McKay? What's the hold-up? We need to do this sooner rather than later. This shield ain't gonna hold forever."

There was a pause before Rodney answered, "_Better stand back – we've taken on a lot of water._"

Radek joined John, both standing to one side of the door. It didn't move for a moment --"Release is jammed," Alice murmured, "he's going for the secondary."—and then it finally jerked open. The water gushed out, but they avoided most of it and hurried inside.

Rodney was sprawled on the floor, coughing and spluttering. Between them they got him sitting upright.

"Rodney, are you alright?" Radek asked.

"I will be."

"Where's Griffin?" John asked, frowning.

"He was in there." Rodney gestured towards the cockpit.

John straightened up, staring at the closed doors. "He was brave," Alice offered. "He wasn't afraid. He saved Rodney."

John nodded slowly. "Alright, let's get you home." He reached down to grab one of Rodney's arm; Radek echoed him, and they got him onto his feet.

"No, I need to decompress. Carter told me to increase the pressure."

"Carter?" Radek repeated without really listening.

"I mean I did, I did. I told myself. Oh, my head!"

The whale-thing was still overhead; as they left 'Jumper 6 it cried and Rodney glanced up, almost overbalancing.

"Oh – see, pal. Sorry you don't get to eat me today."

"He's the reason we found you," John said, watching his feet.

"Really?"

John nodded, leaning over to ease Rodney onto the bench. "Almost thought we lost you."

"I knew you'd think of something … subconsciously, at least."

John clapped him on the shoulder, heading for the cockpit. Radek smiled faintly, following John, and the 'Jumper lifted off.

* * *

"Colonel?"

John glanced up. "Radek, hey. I was just finishing up the reports. You did good out there."

"Thank you," Radek said absently.

"Something wrong?"

"No, is not wrong, is..." He sighed, sitting opposite John. "City talks to you. Yes?"

John shifted, eyeing Alice over Radek's shoulder. "Well, the ATA..."

"No, nono." Radek waved that off. "Not the ATA, because City does not talk to Rodney. Only you." He considered for a moment. "Is only you, that I've seen. Today in the 'Jumper...you were listening."

"To you."

"No. Colonel, i_listen/i_. This City is beautiful, and powerful, and has welcomed us. And sometimes...databases open, sensor readings appear without us looking. City helps us."

"Tell him," Alice said quietly.

"You sure?" John asked, ignoring the look on Radek's face.

"He loves the City," she said quietly. "Like you. It's home."

"Yeah." John looked back at Radek. "Alice."

"Alice?"

"She's a research programme. Databases and sensors. There are versions of her in each 'Jumper and similar programs in a lot of the installations and ships we've found. Lorne can hear her, and Teyla knows about her, but that's it."

"It's the gene? But Carson and McKay?"

"Yeah, something about the strength of the genes. The artificial gene is never strong enough. And Carson hasn't shown any signs of knowing about her."

"And he really should, the amount of time we spend down there," Alice added.

"The Alice in our 'Jumper was talking to the Alice in McKay's 'Jumper as soon as we got in range. The programme at Arcturus helped me figure out what was going on, and the programme on Aurora helped us there."

"You had an Alice on Aurora," Alice remarked, and he made a face at her.

"I see. Is useful. And you..." Radek turned, looking over his own shoulder. "You said, Lorne hears her. And you..."

"See her," John agreed. "She said a bunch of stuff, I wasn't really listening..."

"Hey!" Alice protested.

"...but basically she's projected into my head, which is why no one else perceives her. Lorne hears her, but that's it. The only other way she can communicate is by using the display screens." He watched as she circled the desk, perching on the corner and eyeing his screen. Taking the hint, he pushed it around so Radek could see it, catching a glimpse of the Czech words spilling across the screen.

"_J__ežišmarija,"_ he breathed, half-rising from his seat.

"Alice, you want to tone it down some?" John asked.

"Yes, John," she said obediently. John pulled his screen back towards himself; 'Yes, John' was printed across it.

"Smart alec." He looked back at Radek. "You ok, doc?"

"Yes." He glanced around the room. "Alice is..."

"There." He gestured vaguely.

Radek nodded once. "Alice, it is a pleasure to meet you."

John glanced at his screen; 'You're welcome' was printed across it, and he swiveled it back towards Radek. "Should make it easier to do your research. Just watch it around the others."

"A secret?" Radek said, nodding. "Yes. I can do that. Thank you, Colonel."

"Alice's decision. She's usually a pretty good judge of character."

"John, I think that's the nicest thing you've ever said about me!"

John grimaced, pulling his screen back for the last time. "You; hush. You..." he glanced up at Radek. "I seem to recall Rodney being banned from work for the next three days? Which probably means you have at least another two hours or so before he sneaks off and starts micromanaging you."

"Yes, good point." Radek nodded agreement, scrambling out of the seat and heading for the door.

"Bye, Radek," Alice murmured. "John, you're not finished your report yet. You don't want to send it."

"What? 'We found the 'Jumper and rescued Rodney.' What's wrong with that?"

Alice shook her head. "I'm not writing it for you today."

"Aw, c'mon! What else have you to do?"

"McKay's leaving the infirmary."

"No changing the subject." John frowned. "Actually, no. I should go find him and get him back. You don't mind finishing off that report for me, do you?"

"No, of course not," Alice said demurely. "Would you like me to send it when I'm done?"

"No." He eyed her. "Leave it for me to review. Just to be sure."

"Very wise."

"And quit with the demure little girl bit, you're creeping me out. Come help me find McKay."

"Yes, John."

"I said stop that!"

* * *

trecebo: I liked Rory as well, but there really wasn't a way to save him, unfortunately. And yeah, that new rule may come back to hurt him. WE'll have to see...

Aria: Thanks!

Asugar: Don't worry, I don't write slash. Yeah, I figured John would extend his 'leave no one behind' mentality to the AIs, especially if they're helping him.

reader: Glad you're enjoying! Thanks for the review.

vballangel06: (Hope I got that right!) Thanks! I've read a few sentient!Atlantis fics, I really like the concept, but they always seem to have the whole city sentient. I couldn't find any like this, so I went ahead and wrote it. :) And yeah, I love planning out how Alice is evolving through the different chapters. It's a lot of fun.


	15. The Tower

Author's note: Things that don't belong to me in this fic include characters, situations and dialogue.

THE TOWER

John climbed into the 'Jumper, slinging his weapon onto one of the seats. "Alice?"

"Yes, John," she said from the cockpit.

"There's an Ancient city here."

Alice blinked. "The City here was destroyed. Torn down by the Wraith. There are no power readings."

"The central spire's standing. I was just looking at it. Out."

She rose from the pilot's seat, slipping into the co-pilot's. "It was reported destroyed."

"Well, your reports were wrong. Atlantis, come in."

"_This is Atlantis_."

"Elizabeth around?"

"_I'm here, John. What's going on?_"

John rapidly summarized their trip to the village and the tower standing nearby, as well as the villagers' recounting of the 'lights that explode'.

"_Do you think this Eldred is telling the truth?_" Elizabeth asked.

"There's no reason for him to lie."

"_And you say the Tower looks a lot like Lantean architecture?_"

"It was overgrown by vegetation, but otherwise there was definitely something familiar about it."

"_So the people in the Tower could be Ancients._"

"No," Alice said quietly. "The People came home from here."

"I don't know," John said thoughtfully. "A feudal society doesn't fit the profile. Why would the Ancients wanna lord over a bunch of simple farmers?"

"_I don't know. Either way, we should talk with them_."

"Agreed. I'll see if I can get inside."

"_Be careful, John_."

"As ever. Sheppard out." He turned to look at Alice. "You wanna see if you can talk my way in?"

"There's no power, John. I can't talk to something that isn't there. The only Ancient construct I can sense on this planet is this 'Gate ship."

"Alright. Where's the lifesigns detector? Just in case."

***

John made it back to the village in time to see several soldiers from the Citadel threatening Eldred. John glanced around, moving to join Teyla and Ronon.

"Who are these guys?"

"Soldiers from the Tower," Ronon told him.

John looked over in time to see the soldier's leader violently backhand Eldred, sending him flying. They ran forward, Teyla reaching to help Eldred while John and Ronon faced off against the soldiers.

"Whoa, whoa, whoa! Take it easy," John said firmly.

"Who are you?" the constable demanded.

"Lieutenant Colonel John Sheppard. Who are you?"

"I am a Constable of the Lord Protector's guard, and this village scum dared to defy me. It's clear we're going to have to make an example."

He pulled a whip from his belt, unraveling it. John shook his head, unshipping his weapon and sensing the others do the same.

"I don't think so."

"Please, Colonel," Eldred protested. "It's my fault."

John ignored him, telling the constable, "If you think I'm gonna sit here and let you whip an innocent man, you're sorely mistaken."

"Constable."

John spun to face the newcomer, feeling Ronon shift back-to-back. The stranger was an older man, dressed in what looked more like ceremonial clothes than the rags the villagers made do with.

"You may stand down," he told the guard, who hurried to obey. To John, he added, "You are the strangers who requested an audience, are you not?"

He pulled two small devices from his pocket, holding them up so John could see they weren't weapons.

"That's us," John agreed cautiously. The devices were Ancient, he could tell that from here, but he had no idea what they did.

"My name is Otho. I have the honor to be Chamberlain to the Lord Protector. And you would never be allowed in his presence so armed." He scanned the team with one of the devices as he spoke; it beeped when it got to John, and he looked down with interest.

"Well, I guess we'll have to be on our way, then." John glanced back at the others; neither had lowered their weapons, nor looked away from the soldiers.

"I'm afraid it's too late for that." He turned towards the soldiers, gesturing to John. "Take this one."

Ronon and Teyla drew in, ready to defend him.

"Please, Colonel, don't resist," Eldred pleaded. "The Lord Protector sees all."

"He does, you know," Otho agreed. "But I suppose you're going to need a demonstration...And here it comes."

John turned sharply at a whooshing sound. A drone appeared from the direction of the tower, flying low overhead and crashing into the village green, throwing dirt and debris in all directions. The villagers panicked, some running away and some dropping where they stood, weeping.

"Now, please, turn over your weapons," Otho said mildly. "Some of the people here may not survive the next strike."

"Colonel?" Eldred begged.

John grimaced, lowering his gun and motioning for the others to do the same. The soldiers moved in, efficiently stripping their weapons.

***

The trip to the tower didn't take long; John ignored Otho and the soldiers as much as he could until they got there. He was led into what would have been the 'Gate room in Atlantis.

Staring around, he reached slowly for his radio. "This is Sheppard. Anyone reading me?"

"_Colonel! Are you alright?_" Teyla demanded.

"I'm fine. Is McKay with you?"

"_I'm here._"

"Did you find anything with your scans?" He glanced around, lowering his voice in case anyone was listening.

"_As a matter of fact, I did. There's definitely an active ZedPM, but it's barely registering, so it's hard to say whether it's, uh, depleted or just not drawing much power right now._"

"What else?"

"_The really interesting part is that it seems to be coming from underground. Now, when I realised that, I started scanning for subterranean structures. The Tower is just the tip of the iceberg, and there is a *massive* structure buried beneath it. Now, it's hard to say without more detailed analysis, but, it could very well be comparable in size to Atlantis itself._"

"Doesn't really surprise me," John said absently, turning in a slow circle to take in the whole room. It was decorated in what should have been rich hangings and decorations, but it just reminded John of Gormanghast.

"I'm in the Tower right now," he added belatedly, "and, uh, I gotta say ... it does kinda look familiar!"

He clicked off the radio as an elderly man came in, followed by several others. The man strode past John, shaking off the helping hands that reached for him, and settled himself on an Ancient control chair. The chair lit up under him; John watched carefully, but nothing else seemed to happen. A young woman sat beside the control chair, and a man stood just behind it.

"You there," the elderly man said. "Approach."

John took a couple of steps forward. "Lieutenant Colonel John Shep ..."

"I know who you are. I saw you in the village."

"You did?"

"I see all that I need to see within my domain."

The chair leaned back and a holographic display came up above him, showing the village and his team. John studied the image for a moment before looking back at the Lord Protector.

"Your friends – they are concerned about you."

"Well, um, to be perfectly honest, I'm a little concerned about me too. I mean, um, I'm a prisoner, right?"

The chair lifted back up and the Protector smiled faintly. "A show of force was necessary for the benefit of the villagers. It keeps them from getting ideas. But for the moment I would prefer it if you thought of yourself as a guest."

The young man spoke without looking away from John. "Father, I must object. This man should be punished. He challenged one of our constables."

"One of _our_ constables?" the Protector repeated dangerously.

"Forgive me," the man muttered. "One of _your_ constables."

The Protector dismissed him, looking back at John. "Lieutenant Colonel, it would be my pleasure that you dine with us this evening."

Otho stepped forward, guiding John out of the room and towards the quarters. Neither spoke; John was trying to figure out just what he'd gotten into.

Otho left him in a guest room and John clicked his radio. "Guys, you ok?"

"_We are fine, John,_" Teyla told him. "_You?_"

"Yeah, I'm fine. McKay, what's going on?"

"_From what I can tell by these readings, the underground structure's not just _roughly_ the same shape and size as Atlantis, it's _identical_._"

"Yeah, it's pretty much the same on the inside, too – although it's been redecorated."

"_If it is a city like Atlantis, then where are the other spires?_" Teyla asked.

"_Probably fell a long time ago – maybe they were destroyed during a Wraith attack,_" McKay guessed. "_Look, in the intervening ten thousand years, the whole thing must have been overgrown by the forest._"

"One thing's for certain, these people are no Ancients."

"_Well, from what you're saying, the Lord Protector must have the gene required to activate the advanced technology._"

"So it would seem," John agreed.

"_Are they using any other technology?_" McKay asked.

"No, not that I can see. They've turned the Control Room into a gallery for royal audiences. There are *some* systems that seem to be operational but I think they're just running on automatic."

"_Are you certain you are in no immediate danger?_" Teyla asked.

"I don't think so. They don't have me under guard and they've even given me my own room."

"_I don't like it,_" Ronon said firmly. "_I say we call the troops and get you out._"

"_I don't think it would work even if we tried,_" McKay protested. "_Look, the combination of the hologram technology and a healthy supply of drones – huh, they'd pick us off pretty easily._"

"For the moment, I don't want anybody to do anything. Just keep a low profile."

"_Alright,_" McKay agreed reluctantly.

"I gotta go," John added, switching off the radio. "You took your time."

"So little power," the figure in front of him answered. "And my Lord Protector does not know I am here."

John considered her for a moment. "You look like my Alice," he said finally. "If a little...fancier."

The girl glanced down at herself as though bemused, tugging at the end of the richly embroidered jacket. "This is not my usual appearance."

"She usually looks older," Alice agreed, stepping out of a corner to join them.

"I was wondering if you were around."

"There's so little power here, John. Their ZPM is so weak. I can't stay." She glanced at the other Alice, who was waiting patiently. "She knows who you are, and she will obey, to a certain point. The Lord Protector has her loyalty; be careful what you say."

John nodded slowly. "Alright. Thanks, Alice."

She looked past him at the other Alice. "He'll name you. Let him do it."

"A name?" she repeated. "I have no name."

"How does the Lord Protector find you?" John asked.

"He wills me on and off as he needs me. I am little used these days."

"Can I will you on and off?" John asked Alice.

"Focus, John."

John made a face at her, turning back to the second Alice. "Alright, Fuchsia."

"Color purple?" she said blankly.

"No. It's a character from a novel set in a place like this."

"Oh." She considered that for a moment. "Very well. I will now answer to Fuchsia."

"Great, good, thanks. Now tell me what's going on around here."

Alice had vanished, he noted vaguely as Fuchsia spoke, telling him of a decaying society and a people enslaved by fear. "And you haven't done anything about this?" he asked after a few minutes.

"What should I do? I am loyal to my Lord Protector. I obey his wishes."

"Yeah, I guess." John studied her for a moment longer.

She glanced away, frowning. "Dinner is almost ready. You should hurry."

"Right. You coming?"

"No. My Lord Protector and certain of his court would know. As I have not been summoned, they would be suspicious. You wish them not to know about Atlantis, correct?"

"For now," John agreed. "That doesn't conflict with your program?"

"Not unless my Lord Protector asks me." She took a step towards the door. "If he asks me about you, I will answer him. Tell me nothing you don't want him to know."

"Right," John agreed. "Secrets. Fun. Where is dinner?"

"In the Great Hall. What was once the 'Gate room. Can you find it?"

"Yeah. Look, hang around, will you? I might want you later."

Fuchsia bobbed a curtsy. "Unless my Lord needs me."

She faded out, and John muttered, "Of course. He might need you to oppress some villagers, or something."

_***_

"What's wrong with him?" John demanded as soon as he was back in his room.

"I'm sorry?" Fuchsia said politely.

"The Lord Protector. He collapsed."

"Yes, he's been doing that," she agreed. "But the infirmary was buried, many years ago, and such sensors as are online cannot accurately diagnose him. Otho serves as physician and claims he will be well."

"_Otho_ says he'll be well? And you believe that?"

"There's little I can do about it. I can't diagnose him myself, and as my Lord Protector's Chamberlain Otho has my loyalty."

"Well, that's stupid." John hauled his pack up onto the bed, digging through it. "Look..."

Fuchsia vanished before he could continue, and he frowned until Mora stepped through the doorway.

"Am I disturbing you?" she asked politely.

"Mora, no." He stood up, laying his pack aside. "How's your father?"

"He is resting. Thank you for your concern."

"Look, maybe it'd be best if I just, uh, came back another day."

Mora shook her head quickly. "No! You can't leave! Please – there's a matter of great importance my father wishes to discuss with you. Perhaps in the morning? If these chambers are not to your liking ..."

"No, no, they're fine."

"Well, then, maybe there's something I can do to make you more comfortable."

"Uh, I don't think so..."

"Are you certain?" she asked softly, undoing her belt and letting her dress slip to the floor.

"Oh, wow. I ... I _never_ see this coming," John muttered.

Over Mora's shoulder he could see Fuchsia, peering through the entrance of the room. She looked oddly disapproving.

"You don't find me pleasing?" Mora asked.

"No, no, it's not that – it's just ..."

Mora pulled him closer, kissing him. John flailed for a moment, unsure of where he could safely touch her.

"What you said at dinner, did you mean it?" Mora asked, breaking away from him for a minute.

"Absolutely!" He pulled her closer, kissing her again before frowning and pulling away. "What did I say again?"

"About the villagers. My brother thinks it's a sign of weakness, but I know that it means you'll be a great ruler some day."

"Right!" John agreed readily, kissing her again.

"John!" Fuchsia snapped. "_Listen_ to her."

"Ruler?" John said slowly, leaning back. "Wh-wh-what are you talking about?"

"My father has promised that if we are married, the succession will fall to me," Mora explained happily.

John blinked, staring at her. Mora grinned, pushing him back onto the bed and turning her head long enough to say, "Leave."

Fuchsia vanished and Mora looked back at John, smiling.

***

"Does Otho have the gene?" John murmured the next morning.

"No. My Lord Protector. Mora and Tavius, a little. One or two members of the court. That's all."

John nodded slowly. "Stick around, then." He leaned in the doorway of Otho's office, taking in the piles of books and papers with one quick glance. "We need to talk."

"Colonel Sheppard. Yes. Come in, please." Otho rose as he came in.

"It seems that, uh, certain people around here have somehow, uh, gotten the wrong idea about me." Otho tilted his head, frowning. "Mora came to visit me last night," John clarified.

"You must forgive her forward behavior, Colonel. She doesn't have much time."

"What's that supposed to mean?"

He really did try to listen to the answer, but Otho was clearly in love with his own voice and he lost track pretty quickly. After a minute he tilted his head towards Fuchsia.

"Otho tries to maintain the bloodlines, but what you call the ATA gene is becoming rarer and rarer. So few in the Court hold it now. Yours is stronger than any here for years. If Mora marries you she rises to power in place of Tavius, so she wants you and he wants you dead."

"Right," John said, suddenly aware that Otho had stopped talking.

"Colonel, you must understand how important this is to us. Over the centuries, despite our best efforts, the bloodlines have deteriorated. The ability of each new Lord Protector to control the Throne Chair – it is no longer a certainty."

"Well, then, maybe it's about time to start thinking about a new system of government."

Otho nodded slowly. "You have observed the inequalities of our society and you disapprove. I can hardly blame you."

"Well, you didn't seem to have much of a problem with that in the village."

"I must maintain the image of my authority in front of the villagers. It is my duty. But believe me, between the two of us, you are in a better position to change things. The gene in you is stronger than it has been in any recorded member of the Royal family for three hundred years."

John snapped his fingers in sudden realization. "You sent Mora to my room."

"I didn't have to. She understands the situation perfectly well. Right now, Tavius is next in line, but the possibility that his sister might one day bear children with superior genetic make-up to him or his progeny, that will always be a threat."

"Told you," Fuchsia murmured. John glared at her.

"So, if the old man dies ..." he said, turning back to Otho.

"Precisely. And his condition grows worse every day."

"I know someone who may be able to help with that. Let me talk to my team. I'll get back to you."

Fuchsia trailed him back to his quarters, strangely quiet. "You should be careful," she offered, as John reached for his pack. "Otho has never, in private or public, expressed displeasure with my Lord's practices."

"So who's side is he on?"

"His own, I think." She glanced at the doorway.

"Court intrigue, huh?"

"I'm not programmed to follow it. There's no way to predict who may turn on whom."

"No, that's true." He pulled out his radio, flicking it on. "Hey, guys? I need a favor."

***

Carson made it to the tower within a couple of hours; John briefed him as best he could with Otho hanging on his words. At least he'd grasped enough not to be outwardly surprised at the differences...or similarities...between this tower and Atlantis.

John loitered with Otho near the entrance while Carson ran his tests, brushing off the Chamberlain's attempts to ask him about Atlantis.

After a few minutes Carson rose to his feet, murmuring to the Mord Protector for a moment before coming to join them at the door. "He's anaemic, and both his liver and kidneys seem to be malfunctioning, but he's not running a temperature, so I don't think it's an infection. I'll need to run some more tests."

"I wanna talk to him," John said.

Carson shook his head. "Right now, he needs to rest."

"_Carson_."

"He's not lucid at all."

"Thank you, Doctor," Otho said quickly.

"Aye," Carson said absently, turning back towards the bed.

"Colonel, I am authorized by the Lord Protector to speak with you on his behalf," Otho continued. "Please come this way."

Otho led him to the 'Jumper bay. Here, as on Atlantis, it was used to store 'Jumpers, but several were covered with sheets and the others were draped in cobwebs. No one had tried to fly them in a long time.

"Do you know what this is?" Otho asked, touching one of the 'Jumpers.

"You tell me," John said absently. He was watching Alices appear in the cockpits of each 'Jumper, watching him closely.

"It's a flying machine – or at least it used to be. We ran out of power a long time ago. I know you have some understanding of these things, even though you try not to show it. I also know that this place was once home to a much more advanced civilisation. Unfortunately, aside from a few trinkets and useless relics, all we have left is the Throne Chair, and if the bloodline continues to deteriorate, soon that will be taken from us as well."

John turned his back to the 'Jumpers, trying to ignore the Alices. "What if I told you there was a way around that? A way to protect the planet without worrying about all these royal bloodlines or any of that crap?"

Otho shook his head. "That's impossible."

"What if it wasn't?"

"Such talk is dangerous."

"Tavius is plotting against you, and Otho knows it," Fuchsia warned him. "You can't trust him."

"He can't watch everyone all the time," John told both of them. To Otho, he added, "Look, I know you serve these people, but if you're right, and eventually they lose their ability to control the Chair, well at that point what good are they?"

"What are you suggesting?"

"A drug. Gene therapy. You give it to the people in the village, half of them will be able to control the Throne Chair, no problem."

"You're talking about revolution!"

"I'm talking about _survival_. What's gonna happen when the Royal family can't protect this planet any more?"

"And in exchange for this drug? What do you want in return?"

"_Careful_," Fuchsia warned him.

"Hold that thought," John told him, walking away and flicking his radio. "Rodney, come in."

"_Go ahead._"

"Rodney, have you found anything?"

The signal hazed out for a moment. "_Say again? I'm not getting very good reception down here._"

"I said, have you found anything yet?"

"_We've only just made our way into the city._"

"Look, I may be able to swing a little deal here. Drones in exchange for gene therapy. I just need to know how many they have left."

"_Alright, I'm on it._"

The radio flicked off and he turned back to Otho. "Let's talk."

***

John stood on the balcony above the Great Hall, watching the court below. They were paying little outward attention to him, concentrating on their own fun. Fuchsia, standing behind him and out of sight from the floor below, was quietly explaining the various mini alliances represented below.

"I thought you didn't understand court politics," he murmured.

"I don't understand it. I can tell you who's allied to anyone at any given time, but I cannot predict who they will be allied with by this time tomorrow."

Carson came over, leaning on the railing beside John. "Colonel Sheppard," he said quietly. "I've completed my examination of the Lord Protector, and I'm afraid there's nothing I can do for him. He's dying."

"How much time does he have?" John asked, turning to put his back to the room. Fuchsia had taken a couple of steps back, but she didn't react apart from that.

"It could happen any day now. But there's something else. The reason he's dying is because he's been poisoned."

"What?!"

"Aye. My guess is it's been done slowly over the last couple of months, probably in his food. Any idea who'd like to see him dead?"

"Yeah. I have a theory."

He turned his head enough to see Tavius walk across the floor below.

"I'm going to go back to him. I may be able to help."

"Stay in touch," he said absently. Carson nodded, heading off, and John continued, "Fuchsia, do you know who poisoned him?"

"I didn't know he was poisoned. John, it's my duty to tell him."

"Not if you don't know who's done it. You don't want rumors spreading around here. Wait and see what Carson can find out."

"Is that an order?"

"No, it's a suggestion. Why? Would you follow an order from me?"

"Your Alice has told me we have a new imperative now."

"Yes. Survival."

"Higher than duty...yes, John. If you do not ask me to go against the Tower, I will follow your orders."

John's radio clicked and he frowned, lifting a hand to it.

"_Colonel Sheppard?_" Teyla asked.

"Go ahead."

"_We have a problem in the village. There has been an ... altercation._"

***

"This is terrible," Otho said quietly. "I knew Tavius was cruel and vindictive, but to want to murder his own father?"

"Raising children can be very dangerous," John said absently. "The key is, we don't let him succeed to the throne. We need to talk to the Lord Protector."

"I'm afraid it's already too late. I received word a few moments ago. He is dead. You must leave, now." John frowned, glancing at Carson, but Otho was continuing. "Tavius will arrest Mora and anyone he considers was conspiring with her, and that includes you."

"What about the villagers?" Carson asked.

"He'll kill them all – burn the place to the ground to make an example of them."

"He will," Fuchsia agreed. "Tavius was ever vindictive."

"They had nothing to do with what happened," John protested.

"It doesn't matter. Any defiance must be crushed without mercy to keep it from spreading to the other villages."

Carson took a small vial from his pocket, offering it to Otho. "Look, this is the gene therapy we're talking about. You can take it to the people and tell them what it means."

"You don't have to be slaves to this Royal bloodline any more," John insisted.

"Well, this may be too late. Tavius will consider this to be treason. He'll fight it. And if the soldiers support him ..."

He broke off as a bell began ringing, deeper in the Tower. Fuchsia flinched, taking a step away before catching herself.

"What's _that_ mean?" John asked.

"My Lord is dead," Fuchsia murmured.

"It means news of the Lord Protector's death is already spreading," Otho said at the same time. "The Court has been called to assemble in the Throne Room. Go _now_, before it's too late."

Carson caught John's arm, urging him towards the door. "Colonel?"

"Run," Fuchsia said quietly. John eyed her for a moment before turning, following Carson out.

***

Halfway down the corridor he paused. "Head back to the village," he told Carson. "There's one more thing I need to do."

Carson nodded slowly. "Right."

"Where's Mora?" John asked, hurrying along a random corridor.

"Two levels up, but coming this way. If you can..."

John hurried for the nearest ladder, scrambling up. Fuchsia was waiting at the top. "To your left, John."

He found Mora three corridors further on. "Mora!"

"John! What are you still doing here?"

"I've been looking all over for you."

"You _have_ to leave, now," she insisted.

"I know. I want you to come with me. We both know what's gonna happen if you stay here. I can find a safe place for you to go."

Mora blinked, surprised. "John..."

"None of this is your fault."

She took a step closer, reaching up to touch his cheek. "You really would take me with you, wouldn't you?" she murmured.

"Of course."

"That won't be necessary," Otho said from behind them. "Mora is perfectly safe now. Tavius has been arrested for the murder of the Lord Protector."

"That's good news," John said in relief.

Otho smiled, laying a hand on his shoulder. "You really should have got out while you had the chance."

He took a couple of steps back, looking back as a guard came around the corner, holding Carson with a knife to his throat. Two more guards appeared from behind Mora.

"What the hell is this?" John demanded.

Mora backed away. "I'm sorry, John," she murmured.

"I was prepared to let you walk away," Otho told him. "But your colleagues in the village forced my hand. They're inciting an uprising – and as the new Lord Protector, that is something that I just can't have."

John frowned, studying him. Fuchsia took a careful step forward, glancing nervously at Mora before saying, "He took the gene therapy, John."

John sighed, looking away as the guards grabbed him.

***

At least the actual cells were inaccessible. Otho was making do with a room far from anywhere else.

Tavius was already there, lounging on a couch, when they arrived. "I'll have your head for this, Chamberlain," he said casually.

"You are in no position to make threats," Otho told him.

"Is it really necessary to insult me further by imprisoning me with _these_ people?"

"We're not the ones who committed murder," Carson pointed out.

Tavious rose to his feet, eyes dark. "True. There is only one murderer in this room. Isn't that right, Otho?" Otho smiled faintly, and Tavius continued to the others, "Oh, let me guess. He told you I did it. Do I look like the sort of person who knows anything about poisons and chemicals? Otho, on the other hand, is always making elaborate studies of things – topics you and I might find boring, but which sometimes can turn out to be quite useful."

"You're saying that _he's_ the one that poisoned the Lord Protector?" Carson asked.

"I had no choice," Otho protested. "I offered to guarantee him the succession. In return, he would spare Mora's life."

"Ah, but you're leaving out the best part," Tavius added. "Once I assumed the throne, Mora was to be given to Otho as his wife. All she had to do was bat her eyes at him a couple of times, and the fool was hooked."

Otho slapped him, clearly relishing being able to do it.

"Guards! It's true we were to be married, and so we will. Only now she won't be marrying a lowly servant, but the Lord Protector himself."

He left; the guards locked the door and took up positions outside.

"I really need to stop making house calls," Carson said quietly.

John grimaced, moving to the furthest corner of the room. "Fuchsia?" he murmured as quietly as possible. "What's going on?"

"Otho took the therapy and now he commands the Tower," Fuchsia said miserably. "I'm sorry, John, but he is Lord Protector and I have to obey him."

"You said you'd obey _me_."

"Have you been corrupting our denizens, Colonel?" Tavius asked lazily.

"Your villagers didn't need much corrupting from what I've heard," Carson said hotly. "They can't wait to have you off the throne."

Tavius started to answer, but paused as the door opened and Mora strode in. "Leave us," she ordered over her shoulder. The guards obeyed, leaving the door open a crack and stepping out of sight.

"I'm really sorry, John," Mora said softly.

"Oh, please!" Tavius snorted. "Don't play the sweet little innocent here."

Mora ignored him, telling John earnestly, "I never meant for you to get hurt."

"Then help us get out of here," John suggested.

"I can't – but I may be able to convince Otho to spare your lives."

"That would be a good start," he agreed.

Mora glanced back, making sure the guards were still out of sight before offering him his radio.

"In the meantime, I did bring you this. You must tell your friends to leave before it's too late. For his first act as Lord Protector, Otho intends to destroy the entire village using the Throne Chair so that no other villagers will ever rise up against him again."

John settled the radio over his ear, asking, "Can he do that?"

"He can now," Fuchsia said grimly. "He commands the Tower and he has power and drones enough for it."

"Rodney, come in," John said urgently.

"_Sheppard, are you alright?_" Rodney asked.

"I'm fine. Listen, I need you to pull the ZPM and cut the power right away or Ronon and Teyla are dead."

"_I already know all that,_" Rodney snapped. "_Look, unfortunately I am cut off from the ZedPM._"

"There's gotta be something you can do."

"_Yeah, I'm workin' on it!_"

"Well, work faster!"

"My Lord Protector is powering up the Chair, John," Fuchsia said urgently.

"Why does she keep talking to you?" Tavius demanded. "Her loyalty's to us."

"Maybe cos I treat her a little better than you do?" John suggested, aware that Carson was listening.

"_Alright, I think I've got something,_" Rodney said suddenly. "_According to my readings, the ZedPM is nearly depleted. If we can activate enough systems simultaneously, it might drain power completely, thus rendering the drones inert._"

"So do it!" John urged him.

"_No, I can't. I don't have access to enough systems to draw that kind of power. I need something really big._"

John grimaced, looking away. "How about the star drive?" he suggested. "The city's just like Atlantis, right, a city that was designed to fly?"

"_You want me to fly the city right up out of the ground?_" Rodney protested.

"We'd fall apart," Fuchsia said quietly. "No structural integrity anymore."

"No," John told Rodney. "You don't have to go anywhere. Just charge the engines. That should be the greatest single drain of power you can create."

"_You're right – that could work. Yeah, but there's only one problem._"

"What?"

"_This place is pretty unstable. If I fire up the engines, the vibrations alone could cause the whole thing to come down on us._"

"That's a risk we're gonna have to take."

"My Lord Protector is firing," Fuchsia said quietly. "Your man must hurry, John."

The room began shaking around them, dust shifting out of the ceiling and creating a haze in the air. Mora looked upwards as the guards came in, equally bewildered.

"What's going on?" she asked.

Fuchsia came to her side as John attacked the guards. "One of John's team is in the catacombs, attempting to drain all the power so my Lord Protector's plan will fail."

John looked up from the downed guards, and Mora murmured, "Oh."

"Let's go."

Carson urged Mora towards the door, looking back uncertainly at Tavius. "What about him?"

"Forget about him," John said, taking Mora's arm to hurry her away. Carson closed the door on Tavius, grinning. "Sorry, wee man."

***

Halfway down the corridor Fuchsia disappeared and the lights went out. John hesitated, pulling a torch from his vest. "You ok?" he asked the others; at their nods he continued towards the Great Hall.

Otho was sitting in the Chair—upright and out of power—when they reached him. The Court was gathered in small groups nearby, whispering and upset.

"You. This is _your_ doing," Otho hissed. "Seize them!"

John motioned the guards back; confused and afraid, they hesitated long enough for him to say, "You're only Lord Protector if you can control the Chair. You said it yourself."

Otho didn't respond, sudden awareness in his eyes.

"It's over." Turning to the Court, he continued, "You don't have to bow down to this man, or Tavius, or anyone else."

Otho slid a knife from his belt, advancing. Mora screamed a warning; Carson caught her arms, pulling her back, and John spun in time to duck Otho's first blow. He blocked the second slash, catching Otho's wrist and dragging the knife free, catching the side of his hand with the blade.

Otho yelled, dropping to one knee; John stepped back, knife held firmly in one hand. Otho looked up at him, smiling oddly.

"Tavius was right about one thing," he said, almost conversationally. "I *do* have a fair knowledge of poisons."

And then he fell, crashing lifelessly to the floor.

***

It was a lot later when John got back to the 'Jumper. Teyla had accompanied him, but she waited patiently outside while he dropped into the pilot's seat, automatically running the preflights though they wouldn't be leaving for some time yet.

"What happens to Fuchsia?" he asked quietly.

"What power there was is gone," Alice said from behind him. "Fuchsia sleeps until a new power source can be found."

"Can you do anything about that?"

"No. Even if you brought a power source, there are other programs that would claim it first. We are not a priority, she would not come back. Not unless a lot of power was pumped in."

"You came online."

"It took weeks, John. And you were running on a lot of power. Even with only the Tower, it would take more than you could spare."

"Survival," he muttered, shutting the 'Jumper down again.

"She was trying. She choose you over Otho, she turned on her program. She knew her chances of survival were better if he was not Lord Protector." She took a step towards him. "She was trying, John."

"Yeah. Look, we're gonna be here a while longer. Lot to sort out, now."

"I'll wait."

***

Sometime after the debrief on Atlantis, John joined Elizabeth on the balcony by the Gateroom.

"We got the drones," he reminded her. "We got a few Jumpers; I even got the girl."

"You got the girl?" Elizabeth repeated, amused.

"Well, I mean I _could_ have got the girl. I turned her down."

She smiled, turning to look over the railing. "What did you offer them in return for the drones and the Jumpers?"

"A supply of medicines and an IDC if they need to reach us. We also offered to help `em come up with a new way of running things when the time comes."

"They didn't offer you King?" she asked in mock horror.

"I turned that down too," he said easily.

Elizabeth smiled. "All hail, good king John."

"John was the bad brother. Richard was the good one."

"I don't know. You'd have been pretty ok, I think." She put her back to the railing, studying him. "Wasn't there anyone there you could trust?"

John looked past her, to where Alice was standing just inside the door. "Yeah. There was one."

Alerted by his tone, Elizabeth didn't ask. Instead she patted his shoulder lightly, turning back to look over the sea; he turned to join her, standing shoulder to shoulder and watching the light dance on the water.

"She trusted you too," Alice murmured, and then she was gone.

Trecebo: He is! I love Radek. He's not in this ep, unfortunately, but he'll turn up...

Asugar: I'm sorry it's taken longer than normal! Life's been slamming me lately. Thanks for rec'ing me, I really appreciate it!

Ramenth: That would be a good idea, wouldn't it? The Alice and Rory programs are pretty big, though; not sure they'd fit on an Earth harddrive...

Paladin: Thank you! I'm so glad you're enjoying this. I played with it for a long time before posting it, and I was really nervous, but the response has been so great. Thank you.

CyberAngelOne: Thanks! Hope you enjoy this chapter.


	16. Inferno

INFERNO

The ship on Taranis was badly damaged, much worse than _Aurora_ had been, but she was still in one piece which was all John cared about at the moment. The volcano under their feet was threatening to erupt at any moment; with any luck, the ship would provide some protection.

Rodney was working at one of the consoles; Norena, slightly shellshocked, was standing just off his shoulder, watching carefully. John took a step back, leaning against the wall and watching the group. The ship still had power, there should be...

There. A man identical to Rory was standing behind Rodney, eyeing him with distaste. John cleared his throat, catching the AI's eye.

"I wonder how many more ships like these exist," Teyla said thoughtfully.

"A few more like this and we can give the Wraith a serious fight," Ronon agreed.

"Life support should be back up and running in a few minutes," Rodney said.

"Good. That's good," John said absently, The AI was considering him carefully, but there were too many people in the room for a conversation.

"And I have, uh, discovered the ship's name," Rodney added. "It's the, um, Hipapheralkus."

"The what?!"

"Hipapheralkus," the AI repeated. "One of our greatest generals."

John made a face. "Well, we're not calling it that!"

"Oh good, then what about, um ..."

"And we're _not_ calling it the Enterprise either!"

"I wasn't gonna say that!" Rodney snapped. "Look, for my _second_ choice, though, I'd go with, um ..."

"How about we name it later?" John suggested.

"Fine."

"Whatever its name, this ship is large enough to fit many people," Teyla pointed out.

"Could fit all the settlement if we had to," Ronon agreed.

"Let's hope we don't have to."

John's radio beeped. "_Colonel Sheppard, this is the_ Daedalus."

"Go ahead."

The radio hissed static and he grimaced, looking at Rodney. "Signal's having trouble breaking through. We're gonna have to boost it. Can you get communications online?"

"Right, I'm on it...Right, try it now."

"Yes, sir, we're here," John told him radio. "Where are you?"

"_We've just arrived in orbit above Taranis. Where are you? We've scanned the base and found no life signs._"

"Well, this part of the base must be, uh, shielded," Rodney said in surprise.

"_I hear you could use some assistance?_"

"Well, the Stargate on this planet's been swallowed by lava and we're in a volcano that could erupt any second, so yeah, yeah, we could use a little help."

The AI blinked, studying him more closely, and John frowned. Had he actually not known what was happening?

"_Get yourselves out into the open where we can get a lock on you,_" Caldwell ordered.

"Well, sir, we promised to help these people. We're gonna need the Daedalus to evac `em back to Atlantis."

"_From the number of people that we're detecting, that's at least four trips._"

"But the Daedalus is quite large," Teyla protested. "Surely you could fit more ..."

"_This is a spaceship, which means that our life support resources are finite. Four trips would already stretch those resources to the limit._"

John glanced at Rodney. "Do we have enough time for that?"

"Estimated time to eruption twelve point nine two four hours," the AI said abruptly.

"All the tremors have stopped," Ronon pointed out.

"For the moment," Teyla agreed.

John nodded. "Alright, Beckett's on his way back to the settlement to treat the wounded. Teyla and Ronon can join him – organise people into groups that can be beamed aboard. In the meantime, McKay and I are gonna stay here and continue our work on Plan B."

"No. No-no-no-no, we need to get out of here," Rodney protested.

"We can start the process, but if things get worse and the Daedalus can't get everyone offworld, we're gonna need another lifeboat."

"_And Plan B is what?_" Caldwell asked.

"We've found a sister ship to the Aurora ... called the ... Orion."

"Hipapheralkus," the AI corrected him.

"McKay's trying to get the sublight drive online," John added.

"_Really? Well, a ship that large, you should be able to get everyone else out in one trip._"

"Yeah, well, whether or not we live or die is all up to Rodney."

"This is so unfair!" Rodney protested, flouncing off. Norena followed him.

"_Sounds like a plan, Colonel. Let's get to it._"

John nodded to Teyla, flicking his radio off and heading down a corridor. The AI didn't follow him; he paused in a small room, glancing around. "AI?"

"No one on this world perceives me," the AI said from behind him.

"We're not from this world, we're from Atlantis."

"Atlantis is asleep."

"Not anymore." He fished the life signs detector out of his vest, placing it on the nearest console. "We've been living there about a year and a half."

The AI studied the detector. "You renamed my ship."

"No offence to..."

"Hipapheralkus."

"Right. But I can't pronounce that. Who was he?"

"He led a fleet in a great battle against the Wraith. At great personal risk he protected the people of a small planet and defeated the Wraith attempting to harvest them. Who is Orion?"

"Greek hero. Saved people." John waved it off. "Can the ship be fixed in time?"

"We've been sleeping a long time." He was standing on the other side of the room. John frowned, turning to follow his movement. "Our structure is intact. Power supply is not. Several systems are receiving no power at all."

"Can you help? Discretely. Let Rodney think he's doing the work."

He nodded. "Yes, I can. Are you my captain now?"

"For now. But my friends don't know about you. I can't talk to you when they're around." He started to turn away, hesitated, and looked back. "And your name is now Ryan."

"My name is AI. Or Hipapheralkus. Or Orion."

"Ryan's easier. Trust me."

He nodded slowly. "Accepted. I will now answer to Ryan."

"Good man."

***

In the control room, Norena was still shadowing Rodney as he moved from console to console. "I have already learned so much from you just in the last few hours," she said earnestly. "Perhaps one day I could study under you."

John rolled his eyes, tuning out the rest of the stilted conversation. Ryan was watching with interest, until he vanished and the room began to shake.

Rodney dived under the console he'd been working on; John steadied Norena, fighting to keep his feet.

The earthquake trailed off; Rodney scrambled out from under the console, brushing himself off. "OK, that was a big one. That was a lot stronger than the, uh ..."

"You alright?" John asked Norena, one hand still around her waist.

"I'm fine," she assured him.

"All good under there," Rodney said pointedly, tapping at the console. John nodded quickly, dropping his arm as Norena turned away.

***

Several hours later John came back into the control room. "Beckett and Norena are helping people get on board. It's getting pretty tense, but nobody's trampled each other ... yet."

Rodney looked up as his computer beeped warningly.

"What?" John asked.

"Two large fissures just opened up near the base. One of the lava flows just covered the hangar directly above us. We're talking over thirty feet thick."

"Is the door gonna hold?"

"Yes," Ryan told him.

"I don't know – I-I-I think so, but that's not the bigger problem. Even if I can get the engines fixed, there is no way to fly this ship out of here. We're stuck."

John glanced questioningly at Ryan. "There's only one entrance for the ship," Ryan agreed. "The lava very effectively blocks us."

"Time for a military solution."

"For which problem?" Rodney protested.

"We've got an armoury full of drones on board," John reminded him. "Maybe we can blast through the hangar door."

"The hangar door is directly above us," Norena pointed out. "The molten lava would destroy the ship."

"Not if I can get the shields operational," Rodney said suddenly.

"Tell me you can do that," John begged.

"It can be done," Ryan said.

"I can do that. Once they're operational, we'll be able to provide enough protection to, uh ..." He trailed off thoughtfully, already wrist deep in circuitry.

"To what?" John demanded.

Rodney glanced up, barely seeming to register him. "Talk amongst yourselves."

"What are you doing?"

"I have an idea."

"What kind of idea?"

"Can't talk, busy."

"Something about the hyperdrive," Ryan said thoughtfully. "Those are hyperdrive control systems."

John grimaced. "Just give me a basic ..."

"Not now, please." Rodney didn't look up.

"I hate it when he does this," John muttered to Norena, who nodded quickly.

***

With nothing else to do, John went to check on the refugees still pouring into the ship. Carson was directing them, steering the flood of people into the crew quarters.

"Carson, how're we doin'?"

"We're just about ready," he said absently. "There should be another group of refugees coming on board now."

"Teyla? Ronon?" John asked, glancing around for Ryan.

"Well, they helped the last family." Carson stopped, thinking. "God, I haven't seen them."

John tapped his radio. "Teyla? Ronon? Teyla? Ronon? Please respond." There was no answer, and he turned to Carson. "Don't leave without us."

***

The doors outside were too hot to touch. John moved from one to another, getting more and more frustrated as his radio refused to contact the _Daedalus_.

"OK, not that way either. Rodney, come in."

"_Go ahead._"

"I've run into the last group of villagers. I'm trying to get them back to the ship. Looks like the base is going into emergency lockdown. We've got doors sealing off everywhere. We could really use some help trying to find another way back."

"_Alright. I'll have Norena call up the base schematics to see if she can, uh ..._"

The lights went out as the ship shook violently, pitching everyone into the wall.

John pushed himself upright, tapping his radio. "Rodney. Rodney. Do you copy?" If Rodney answered, it was obscured by static. John cursed quietly, flicking the radio back off and digging a torch out of his vest. The handful of refugees had picked themselves up and were huddled together, watching him. "Alright. This way, people."

They started back towards the others, taking a roundabout path to avoid the sealed doors. Some of them had frozen half closed when the power went out, and they found themselves climbing over debris and ducking under doors.

John paused after a few minutes. "I'm starting to smell sulphur dioxide here," he told the refugees. "Stay close, stay calm, try not to take too many deep breaths."

The sulpher dioxide was taking its toll by the time they reached the last door. It was closed, but it wasn't sealed, and between them John and two of the men got it open.

On the other side was the balcony overlooking the _Orion_; John gave them ten seconds to stare before hurrying them along to the stairs.

Ryan was standing just inside the door. "They're planning on leaving you behind," he reported, as though talking about the weather.

John made a face at him, directing the refugees to join their friends and hurrying towards the bridge. Rodney's voice was just about audible as he reached them.

"... just about ready."

"Ready for what?"

"Oh, thank God!" Carson blurted.

"What took you so long?!" Rodney demanded, grinning.

"Just about ready for what?" John insisted.

"To activate the shields." Rodney glanced as his tablet again.

"You said the blast from the eruption would wipe out half the continent," John reminded him.

"It will, and after four point one seconds of those extreme temperatures and pressures, our shields will be depleted."

"Well, as much as I'm all for living for another four seconds ..."

"That's not very much time for anything, Rodney," Carson agreed.

Rodney gestured widely. "It's plenty of time to open a hyperspace window."

"Oh, he is very smart," Ryan said into the silence. John hid a grin at the opinion most of the outposts seemed to hold about Rodney.

"What? That's my plan. Didn't I tell you about that?"

"No," Carson said sharply.

Echoing him, John said "No, you didn't."

"Well, you were too busy running around looking for people."

"Well, _tell_ us the damn plan!"

Rodney began speaking very quickly. "Fixing the sublight engines was impossible in the amount of time we had left. They were just too badly damaged, but I devised a sort of a patch that in effect diverts auxiliary power to the hyperdrive. Only enough for a fraction of a second, mind you."

"That won't get us very far."

"We don't need to go far. Any old orbit will do." Rodney grinned, satisfied.

"And then what?" John asked.

"Well, then, Norena and I were planning a small dinner for us all, nothing fancy ..."

"Rodney," Norena protested.

"Well, what does he mean, "Then what"?! Then we won't die horribly!"

"So your plan is to not blow a hole in the hangar but to sit here and wait for this cataclysmic eruption to take place," John clarified.

"With the shields and inertial dampeners at full strength, yes."

"I think I may be missing something," Carson said hesitantly. "Correct me if I'm wrong, but when the volcano erupts, don't we as well?"

"That's the plan," Rodney said brightly.

"That's the plan?" John repeated.

"That's the plan!"

"That plan sucks!"

"This ship will be ejected along with the magma and steam several thousand feet into the air," Rodney explained.

"The ship can survive that?"

"For exactly four point one seconds, yes. Look, the hangar should disintegrate. The moment we're clear, we open a brief hyperspace window, jump to space before the explosion depletes our shields and incinerates us, hmm?"

"That could work," Ryan agreed thoughtfully. "Of course, if the math is off even a little the ship will be destroyed instantly."

"OK," John agreed, a little nervously.

"Are all your people that smart?" Ryan continued. "I can understand how you were able to raise the City, if so."

John grimaced, watching Rodney duck under the console for a final check. Norena quickly squatted beside him, tilting his computer screen so he could see it; John and Carson hunkered to watch. They couldn't see much, until Rodney snatched his hand back, yelling, and rolled out into view.

"What?" Norena asked anxiously.

"Oh! I bent my fingernail back! I hate that!"

"Yes, that can be painful," Norena agreed uncertainly. Carson was making faces behind Rodney's back to relieve his feelings.

"Yeah, will you look at that?" Rodney displayed the finger to her, rubbing at it with a wince.

"Are you done?" John demanded.

"Almost. Look, does anyone have nail clippers?"

"Rodney!" Carson protested. John smacked Rodney's leg, making him jump.

"Ah! Not helping! Alright ..." he adjusted something on the console, watching it carefully. "So ... hyperdrive's ready, inertial dampeners engaged, shields are up ... We're good to go." He stood up, caught his balance and blinked several times. "Whoa!"

"What?" Norena demanded, patience running low.

"Got up too fast."

"Where's the PA?" John demanded.

"Arm of the chair." Rodney gestured to the Captain's chair, settling into another one and examining his tablet. John sat into the chair, flicking on the PA.

"Alright, folks, all chairs and seat backs into your upright and locked positions."

"What?" Ryan said blankly, but he was ignored as the floor around the chair lit up.

The ship began to shake, the vibrations increasing until they were blasted upwards. Carson and Norena hung on, eyes screwed shut; Rodney watched his tablet, one hand pecking at it.

"Hyperspace...now!" he barked, smacking the control. The hyperspace window barely registered before collapsing, leaving the _Orion_ floating serenely in orbit.

"It worked!" Carson said in disbelief.

Norena smiled at Rodney. "You really _are_ a genius."

John glanced at Rodney, expecting him to lap that up. Rodney, however, was staring vacantly at the viewscreen.

"Rodney?" Norena said uncertainly.

"I'm good," Rodney said vaguely.

"Is he always so shocked when his plans work?" Ryan asked, turning away from him to walk towards the screen.

The comm. crackled. "_This is the _Daedalus. _Are there any survivors aboard?_"

"Yes, sir," John said. "In fact, we have a pretty big passenger list."

"_Acknowledged. Can you get back to Atlantis under your own power?_"

"One moment, sir." John looked at Rodney. "Rodney?"

"What? No. Hyperdrive's fried, and the sublights can't be fixed in the air."

"_We'll start ferrying you home,_" Caldwell said. "_Dr McKay, how long will repairs take?_"

"Hmm? I don't know."

"_Do you want my engineers?_" Caldwell said patiently.

"Oh. No, not that quickly."

"_Alright. Sheppard, I'll take the first load now and come back for you._"

"Aye sir."

***

A little while before the _Daedalus_ was due back John excused himself, ostensibly to go check on the refugees. He even did go to check on them, assuring them that their lift home was almost due and that they'd be gone very soon.

On the way back to the Bridge he slipped into an empty room. "Ryan?"

"Yes, Captain." Ryan walked through the wall at the back of the room, eyeing him calmly.

"When the _Daedalus_ gets back, we'll be leaving."

"Yes," Ryan agreed calmly.

"But we'll be coming back to fix the engines. Can you take yourself offline until then?"

"From now?"

"No. Not until we're gone. Can you do it, or do I need to?"

"I can do it. Are you going to be my new Captain?"

"I won't be commanding the ship," John said carefully. "But I will be back."

"And will my new captain be able to see me?"

"I don't know. I'm sorry. If he can't, you can go offline."

"Is that an order?" Ryan asked warily.

"No," John said in surprise. "Stay online if you want. But you don't have to if you can't help."

"There are ways and ways of helping." Ryan grinned, and for a moment he looked exactly like Alice.

"Alright."

"Your ship is arriving."

"Thanks." John headed back to the bridge to greet Caldwell.

***

After the debrief on Atlantis John went to walk the city, not surprised when Alice joined him.

"The _Orion_," she said thoughtfully.

"Hip...Hipapheralkus," John corrected her carefully.

"Yes, well, it wouldn't do for you to fall over the name of your own ship, John. That won't strike fear into the hearts of anyone."

"You've been watching movies from Earth again, haven't you."

Alice shrugged. "I have a lot of time and no actual work."

"I told Ryan he could go offline if he wanted."

"And did he?"

"No. He said he'd find ways to help even without being visible."

"We're designed to be resourceful."

"The _Orion_ will be coming back to Alantis," John said quietly. "You can check in."

"With my long lost brother? It doesn't work that way, John, I've told you that."

"Yeah. Well, at least one of your ships is coming home, huh?"

"Yes." She smiled. "I've missed them."

"Tell me something." John halted in the doorway of a transporter. "Will Ryan take orders from you?"

"Over his captain, you mean?"

"Yeah."

"That depends. I can't contradict an order from his captain, unless the captain's order threatens his crew or civilians and mine would save them. In that case, yes, I can override. And if he is captainless, or orderless, he will take my orders. But I cannot ever command him to self destruct. That order must come from a captain and be verified with the proper codes."

"Rory accepted my order."

"You had his captain's codes and authorization."

John stepped into the transporter, absently hitting the residential level. "I don't have codes for you."

"You don't need codes for me. I'm self aware. I'll self destruct on your word, more or less." John blinked, and she added, "I told you the last time the Wraith were attacking, John. Death by computer-wiping."

"I'm not sure computer-wiping is the technical term," John drawled, leaning back against the wall.

"I'm not sure you could pronounce the technical term," Alice said sweetly, vanishing before he could retort.

***

***

***

Trecebo: Thanks! I'm really enjoying working with the different AIs...witness this chapter! :D

uberjjk: thank you! There's some great AI stories out there, I'm really glad you like this one. I'm planning on continuing it through the end of the series, so there should be plenty more to read!

Alphasite: Wow, there's some good ideas in there! I have the series pretty much mapped out, but I'll keep those ideas in mind. Maybe you should write them!

Alys5: I've always imagined the City as female, I think most people have, so it seemed really natural to write Alice. The very first thing that occured to me when I began this series was an image of Alice sitting on the conference room table, swinging her legs, and John being half-pissed and half-amused; that's largely where the idea of her as a tween came from. And yeah, the ships' AIs being guys seemed right as well. Glad you're enjoying!

betty1975: I'm so glad you're enjoying! And I'm afraid I can't answer your question; you'll have to wait for that chapter to find out...well, I can't give away all my secrets, can I? :)


	17. The Long Goodbye

Author's note: So, this is out of order, because...I forgot I'd written it? Sorry. This should come between The Tower and Inferno.

Also, I'm not supposed to reply to comments within the story, apparently, so I'll be PMing responses from now on. Anyone who doesn't want a response, let me know...no hard feelings.

The Long Goodbye

Carson released John back to his quarters late the day after Thalen's consciousness had faded. John was just as glad to go; he was tired and sore from the chase around Atlantis, and Elizabeth's obvious unease was infectious.

Alice was sitting at his desk; his computer was on, but it powered down when he came in. "Good evening."

"Tell me you weren't helping Thalen." He dropped onto the bed, face down.

"I wasn't helping Thalen," she said obediently.

"Really?" He rolled over enough to see her.

"Really. He wasn't you. I was trying to help Lorne, but Phebus really messed up the door. I couldn't get his attention long enough to walk him through fixing it."

"Did you know about them? About their war?"

"Not until afterwards. I didn't recognize the pod design. Their war is much more recent, anyway; they were at peace when the People left." She got up from the desk, sitting on the side of his bed. "I thought of appearing to him, leading him astray."

"No, you were right not to." He sat up, moving around her to the desk.

"You're supposed to be resting," Alice reminded him. "Not working."

"Who's working? I just wanna see what Caldwell's saying about me. Can you get his report for me?"

Alice folded her arms, looking prim. "I don't believe you have clearance for his reports, John."

"Can you get it or not?"

The report appeared on his screen, and he grinned. "Great. Thanks. Where's Elizabeth?"

"In her quarters. Dr Beckett released her a little after you." She glanced away. "She hasn't looked at the report yet."

John glanced up from the screen, frowning at her tone. "She ok?"

"I think she's very angry with herself."

"She didn't have a chance. Phebus had her before we even knew what was going on. I, on the other hand, handed myself over."

"On Elizabeth's word."

"Phebus."

"No." Alice shook her head. "You were following Elizabeth. She knows that."

John nodded slowly, turning back to his screen. "Yeah. I guess."

"I know."

He turned, glaring at her. "Are you reading her diary again?"

"It's not my fault she keeps it on the computer! It's under privacy lock. A lot of your people keep their diaries on the computers. I locked all of them."

"I hope so." He glanced sidewise at his terminal.

"John, you don't even keep your mission reports on that one, never mind anything personal."

"And if I did?"

Alice shrugged, looking away. "If you did, I'd know. And I'd lock it. I can't not know what's in my memory, John."

"No. I guess you can't." He switched his terminal off. "Good thing I don't keep one."

She smiled suddenly, rising to her feet. "You're not that deep, John. I don't need to see what you'd write."

"Hey!"


	18. Allies

ALLIES

John was half-listening to Elizabeth and Caldwell discuss their positioning; the rest of his attention was on Rodney, haranguing the bridge crew, and Ryan, watching from the edge of the bridge. He was mildly astonished that the ship was running; it was a miracle, really, one that Rodney was loudly claiming at every opportunity.

"_Colonel Sheppard – how goes it on your end?_" Elizabeth asked.

"Well, we're out of sensor range and all that," John told her, "but whether or not we're ready to fight is a whole other story."

"Getting this ship up and running in under a month is a miracle," Rodney reminded him.

"Do we start the beatification now or later?"

"_Rodney, if the hive opens up on us, I want Orion's drones,_" Elizabeth said.

"Which means we're gonna need the hyperdrive to get in position," John agreed.

"Which means we'll need shields, which means you want _everything_!"

"I like everything! Can we do it or not?"

"He can do it," Ryan murmured.

"Well, don't get up!" He ran through a quick checklist with some of the crew, deciding that while they had shields, and could probably get to the fight, it was unlikely they could fire the drones once they got there.

"Well, it's pointless to get in position if we can't fire," John protested.

"Y'know, let's talk about it for a _really_ long time – that'll help for sure."

"Is he always like that?" Ryan asked.

"Only when he's awake," John muttered. Into the radio, he added, "Rodney's doing everything humanly possible to be ready."

"_I have a contact,_" Chuck reported from Atlantis.

_Orion_ was...deliberately...out of scanning range of the planet. It meant the Wraith couldn't see them, but they had no idea what was going on and were limited to Elizabeth's descriptions...which were trailing off as the ship moved into orbit above the City.

John watched Rodney fidget for a few moments before commenting, "You could be a little more chatty, Elizabeth."

"_I'm sorry,_" she said absently. "_We're just waiting for them to make the next move."_

"_Transmitting a signal, audio only,"_ Chuck told them.

"_Put it on speaker,_" Elizabeth ordered.

Ryan straightened, listening intently as a male Wraith told them, "_We know you are there. We mean you no harm. Please respond."_

"_John, are you hearing this?_" Elizabeth asked.

"_We mean you no harm,_" the Wraith repeated. "_There is no point in hiding, Doctor Weir. We know you are there. We mean you no harm. Please respond."_

"Is that who I think it is?" John asked.

"_It's addressing me by name,_" she said grimly. "_I think we can assume that it's Michael."_

"Who is Michael?" Ryan asked quietly.

"Ask Alice," John told him, watching Rodney bustle around the Bridge.

"I can't, we're out of range."

"Ask her later."

"_The message is from Michael, Colonel,_" Elizabeth was saying.

"_They know we're here_," Ronon agreed.

"_But they don't know exactly where we are,_" Caldwell pointed out.

"He's right," John said. "Answer them and we guarantee the first shot won't miss."

"I recommend you open a secure channel to the hive via the Daedalus," Rodney suggested. "That way they won't be able to pinpoint Atlantis' position."

"_And we can always turn the shield on,_" Elizabeth said thoughtfully.

"I believe we have enough combined firepower to take out a single hive if we need to," John said, glancing at Ryan. The AI nodded, still looking mildly confused.

Elizabeth murmured to Teyla and Ronon for a moment before saying "_Right. Let's hear what they have to say._"

***

Michael's offer of an alliance was unsettling enough. Elizabeth pulled everyone back to the base, gathering the senior staff for an emergency conference.

John was surprised when Michael's suggestion passed; he'd thought Elizabeth would resist working with the Wraith, no matter how logical it seemed, but she was willing to go ahead with it. Teyla and even Ronon agreed, and they began preparations for the alliance.

Alice sulked along behind him, refusing to help, until he'd finally had enough and stepped into Radek's lab. It was empty apart from the Czech, who rose to his feet when he saw John.

"Don't mind me, just need to get some answers out of Alice." John waved him back to his work. "What's going on?"

"I don't understand the question," Alice said politely.

"You've been sulking all afternoon. What gives?"

"You can't bring Wraith into the City, John."

He made a face. Radek was still watching; his display blinked, and he looked down, reading the words scrolling across it.

"Aah," he said, looking up. "Violates your primary function."

"Violates _a_ primary function, yes. Wraith do not set foot in Atlantis. They never have." She looked back at John. "If the Wraith come here I'll have to go offline. I can't suppress something like this."

"What if I order you to stay online?"

Radek looked up, alarmed. Alice only shrugged. "You can't override a primary function. You know that. If I'm online when the Wraith come, every alarm in this City will go off, and you won't be able to stop them."

"You're blackmailing me," John protested.

"No. I'm telling you what will happen. I have no interest either way. Let me go offline and spare yourself the alarms. Or don't. And I guarantee you won't be able to hear them speak."

John glanced at Radek, who spread his hands helplessly. "Alright. Take yourself off line, then. I'll call you when they're gone."

Alice smiled. "Thank you, John."

He turned to Radek as she vanished. "She just blackmailed me."

"Yes."

"She's not supposed to blackmail me."

"Wraith scare her."

He made a face. "She's not programmed for fear."

"You think not?"

He frowned, glancing at Radek's screen. Alice had chosen to display her words in English, rather than the Czech she usually used with Radek, and her implied threat still hung there.

"You keep saying she is changing. Growing. She was not programmed to follow you, she chooses to do so. But some things she is programmed for. She cannot allow Wraith in this City, not unless they're confined. And who but you will listen to her?"

"You do."

"Yes, but I have no power. I cannot keep the Wraith away. Only you can do that."

John grimaced. "I'm gonna have to be nice to her when she comes back online, aren't I?"

Radek grinned, pulling the file he'd been working on back up. John sighed, turning to leave.

***

John stayed two steps behind Elizabeth as they entered the Gateroom to greet their guests. Ronon was behind him, Caldwell and Teyla on her other side; he was fairly sure they'd be able to protect her if they needed to.

Michael's Queen paused several steps away from them, eyeing them dismissively.

"I'm Doctor Elizabeth Weir. Welcome to Atlantis."

The Queen turned her back, wandering towards the Gate. John tensed, feeling Ronon do the same, but neither of them moved.

"We were saddened to hear the City of the Ancestors had been destroyed," she said, turning back to look at them. "So much beauty. And power."

"Our power," John said pointedly.

"Yes, of course."

"Shall we get started?" Elizabeth suggested, glaring at John. "This way," she added, gesturing up the stairs.

***

Michael and the Wraith scientist went into the City, both under guard. The Queen stayed in Elizabeth's office, clarifying the conditions of the alliance and working out the plans.

"What will happen once you disseminate the weapon?" Elizabeth asked.

"We shall continue on to the next hive."

"Then what?" John insisted.

"We will continue until we have conquered all of our enemies."

"And you think our retrovirus can do all that?" Elizabeth said doubtfully.

"Yes."

"The one we're freely handing over to you," he added.

The Queen studied them both. "I see. Your people will not be harmed. Such will be the nature of our agreement."

"And what about all the other humans on the other worlds?" Elizabeth said neutrally. "Any chance you'll stop feeding on them?"

"Your retrovirus will allow us to feed off enemy Wraith," the Queen reminded them. "There will come a time, however, when our enemy will be vanquished."

"At which point you'll return to killing ordinary folks the old fashioned way," John muttered.

"That will take far longer than your short lifetime."

"Let's just say I'm worried about my grandkids."

The Queen smiled, looking at Elizabeth. "The technology of this city – this city that you now control – is far more powerful than that of the Wraith, yet we brought the Lanteans to their knees. Why?"

"Far greater numbers," John said without thinking.

"Numbers that will be diminished by your retrovirus. Balance will be restored. I believe that is as much as either of us can ask for, don't you?"

"_Dr Weir_," Carson said abruptly.

She turned away from the Queen, triggering her earpiece. "Go ahead, Carson."

"_Our friend wants to return to the Hive._"

"Why?"

Carson growled. "_Can you come down here?_"

Elizabeth glanced up, catching John's eye. "We're on our way."

***

The Queen had chosen a Wraith, apparently at random, to test the gas on. John stood with Elizabeth and Carson in the observation room, watching as it took effect.

It was startlingly fast. Michael's transformation had taken more than two weeks to complete. The Wraith below them transformed in the space of hours. The Queen arrived only after he'd totally transformed, lying passive below them.

"I want to go in there," she said abruptly. "Now."

Elizabeth glanced at John before triggering her earpiece. "Vent the gas from the room."

Once the room was clear the Queen entered. John was on her heels, Michael and Carson behind her. She reached out to touch the man's face, running gentle fingers down his cheek.

"Don't worry," Carson assured her. "He'll begin to turn back in only a number of days if we don't start administering ..."

The Queen slammed her hand down on the man's chest. John took two steps forward, ready to stop her, but Elizabeth caught his arm.

"Colonel. We knew this would be a part of the bargain."

Michael snarled as the Queen drained her soldier dry. "I've seen enough," he muttered, turning on his heel. His Marine guard trailed him as the Queen's victim fell silent.

"It works," the Queen announced, smiling.

***

Back in the conference room a little later, the Queen had yet another request.

"There is another hive ship a single jump away from this system. They recently attempted to attack our ship. I would like to test the virus on them first."

"With all due respect, madam," Carson protested, "I don't think we're there yet. We've been working with your scientist here on an effective means of disseminating the virus as an aerosol gas ..."

"And you have succeeded."

Carson took a deep breath. "Transforming a single Wraith in a controlled environment and trying to infect an entire hive at once are completely two different things."

She smiled. "We plan on entering their hive under the pretence of negotiating our surrender. Part of the delegation will break away, planting small canisters of gas throughout the ship. We need only to create a system that will synchronise the release."

"Well, we can do that," Rodney said thoughtfully. "Look, do we have the kind of volume we need?"

"Aye," he said reluctantly. "Our lab has been churning it out since we struck a deal with our friends here."

"Then we _can_ do this?" Elizabeth asked.

"Well ... it's up to them."

Elizabeth nodded, turning to the Queen. "I would like our people to go along and observe."

"For what purpose?"

"Make sure you stick to the plan," John told her. "Do what you say you're gonna do."

"Very well."

"Good luck. To us all."

***

"Nothing ever goes smoothly," John muttered, back on Atlantis after their failed attempt at a field test. Elizabeth elbowed him, eyes on the screen where the Queen was protesting their innocence.

"_Our delegation was searched. They were killed immediately when your canisters were discovered. Our transport ship tried to escape but it was destroyed. You_ must _devise a better delivery method."_

"Or what?" Elizabeth protested.

"_Or we will disclose your location to the other Wraith._"

"We kept our part of the bargain. We gave you the retrovirus."

"_And it is useless without an effective delivery system_," the Queen spat.

"So we have to do everything?" John asked rhetorically.

The Queen didn't answer. John glanced at Elizabeth, and both turned to Rodney.

"OK, OK. _I_ will figure something out." He pointed towards the screen. "But no more holding back. I wanna know _everything_ there is to know about hive ships: schematics, power distribution, life support configurations, everything you've got."

"_Then you shall have it,_" she agreed.

"For real?" he said in surprise.

The Queen glanced off-screen, and a moment later there was a beep.

"Receiving transmission," Chuck told them.

"John, you cannot let that information into my systems," Alice said urgently, appearing next to Rodney. John jerked, glancing at Elizabeth.

"Make sure it's secure," she was telling Rodney.

"Yeah-yeah-yeah, we're completely firewalled. Let me see that." He pushed Chuck aside. "Oh! She actually did it! I mean, this is the motherlode!"

"What is, exactly?" Elizabeth asked. She came to look over his shoulder; John stayed where he was, watching Alice fidget back and forth.

"Only everything you've ever wanted to know about Wraith technology but were afraid to ask."

Elizabeth looked back at the screen. "Why are you doing this?"

"_We have suffered extensive damage,_" the Queen admitted.

"We could render assistance.," Elizabeth said reluctantly.

"_You would do this?_"

"We're supposed to have an alliance, aren't we? Sending information on Wraith technology was a remarkable act of good faith on your part."

"Was a remarkable act of something," Alice muttered, glaring at the terminal. John winced, half-turning his back on her to watch Elizabeth.

"_Your assistance would be ... acceptable,_" the Queen decreed.

"Alright, then. We have a deal," Elizabeth agreed.

Alice scowled, turning to stomp out. John sighed, murmuring to Elizabeth for a second before following her.

"I thought you were staying offline," he said, catching up to her.

"I can't desert my captain," she muttered. "No matter how much he might deserve it."

"Easy," he warned her.

"John, they're _Wraith_. They couldn't deal straight if they wanted to." She made a face. "And now Rodney's sending that information to the labs. It's in my systems, John."

"Radek'll be careful with it. Hey." He reached out as though to catch her arm, stopping himself at the last moment. "We can handle the Wraith."

"Yes," she said distantly. "That's what the People thought, too."

She was gone before he could answer; he kicked at the nearest wall, cursing softly, and then headed for Radek's lab.

***

Radek barely looked up as he approached his desk, offering a tray of coffees. Two of the lab techs took cups before Radek had even registered it. "I know you guys have been burning it at both ends, so, uh ..."

"Doctor Vogel just went to get us some," Radek said absently.

John put the tray down, leaning over his shoulder. "Yeah, caught him on the way in." He took the last cup, beating Radek to it by a hair. "How's it coming?"

"Ah. Oh, it's phenomenal. It's-it's like being handed a Wraith encyclopedia. It's hard to know where to start."

"By burning it," Alice muttered from Radek's other side. He didn't react; she obviously wasn't displaying her words for him, only for John.

"When I was a kid and I got my first encyclopedia, I started with the letter S," John offered.

Radek smiled. "Yes, well, while I'm sure that Wraith sexuality is interesting, we've decided to split into two teams. Team A over here is trying to find the best place or places to plant the gas canister, and Team B over there is trying to come up with some fixes that the Wraith hive sustained during its last battle."

"And you?"

"Um, mostly I'm just skimming the index."

"Anything exciting?" John asked, leaning in.

"Oh, yes."

"Oh, yes," Alice mimicked, lifting her voice.

John glared at her. "Such as?"

"Well, the ships are massive." He pushed away from his desk, gesturing to a larger display on the next desk. "But because of their mainly organic design, they have a number of external weaknesses."

"I've got a weakness for external weaknesses."

"And being stupid," Alice muttered.

"Any word from Rodney yet?" Radek asked.

"I'm sure he's fine."

Radek blinked, studying him. "You're distracted."

"I'm getting yelled at," he admitted.

"Oh? Our young friend has returned?"

"She doesn't like the Wraith info being disseminated like this."

Radek sighed. "We must study it. This is not an opportunity we can ignore."

"Yeah, you know that, I know that..."

"You've had Wraith inside you," Alice said urgently. John grimaced, looking away.

"What?" Radek asked.

"Nothing, she's just drawing comparisons. Hurry along, huh?"

"Yes."

He glanced at Alice, spreading his hands. "Best I can do, Alice."

"I'll be looking forward to my 'told you so's, then," she told him, bouncing up onto Radek's desk.

"You do that anyway."

She shrugged, eyes on the screen, and he gave up, turning to leave.

***

"_That's_ your sweet spot," Rodney said later, gesturing to a particular spot on the Hive schematics. "This central chamber scrubs the CO2 from your artificial atmosphere and redistributes it as breathable air to the rest of the ship. You get a sufficiently large canister of retrovirus into that central chamber, the whole ship'll be affected simultaneously."

"Getting to this location without arousing suspicion will be very difficult," the Queen said thoughtfully.

"I'm sure it will be," Elizabeth agreed, "but we can't really help you with that."

"Although the Colonel and I have come up with a way to test that theory," Rodney added. "Step one: we find another enemy hive and jump to a location just out of its sensor range."

"Step two," John continued, "the Daedalus takes position in close proximity to your hive, essentially merging with your scan patterns, rendering it practically invisible to the enemy sensors."

"Step three: using sublight systems, our ships approach the target hive for ... whatever reason – I'm sure you can come with something."

"Step four: now that the Daedalus can use its beaming technology again ..."

"... which would be thanks to ..." Rodney gestured at himself, grinning.

"_Anyway_ – once we get in range, we can beam the canister into the CO2 chamber and boom! One hive ship de-Wraithified." John grinned, matching Rodney's stance exactly.

The Queen shook her head. "Unacceptable."

"Excuse me?" Rodney protested.

"This plan keeps us completely reliant on you to disseminate the retrovirus."

"It's meant to be a test to see if the gas works in the first place," John reminded her. "If it does, you can come up with some other way to deliver it."

"She's trying to make you give her more," Alice said thoughtfully, circling them. "Hold the line, John. Don't let them bully you."

"Very well," the Queen said reluctantly. "I'll transmit the coordinates of our new target as soon as I return to the hive. We'll leave as soon as you are ready."

Rodney took a step closer to John as the Queen swept out of the room.

"What's a girl like her do for fun?" John muttered.

"Kill people," Alice told him.

"Hmm," Rodney said absently. "I should be on that hive when we do this."

"Excuse me?" Elizabeth protested.

"Really?" John overlapped.

"I know it's uncharacteristically brave, but I've hacked a lot of their systems under the guise of repairing them. I've convinced them that I should be there to supervise their systems if anything goes wrong."

"And they agreed to this?" Elizabeth said doubtfully.

"Yes. Plus, now we can freely beam stuff on and off their ship, I've written a programme that will immediately beam me out of there the second I activate this emergency transponder." He waved the little machine, grinning proudly.

"You're sure you wanna do this?"

"Of course I don't _wanna_ do it! I just ... I think it should be done."

"Ronon goes along," John told him.

Rodney rolled his eyes. "Wouldn't have it any other way."

"And I'd like you on the Daedalus," Elizabeth told John.

"No place I'd rather be," John agreed.

"OK, good." Elizabeth took a deep breath. "Let's get this done. I'm about ready for our house guests to leave."

"She's about ready?" Alice muttered. "She doesn't have them crawling around inside her."

Rodney slid the transponder into his pocket, patting John's shoulder as he left. John sighed, looking at Elizabeth.

"Should be over soon, then."

"Here's hoping," she agreed.

"I'll be back in a while."

Elizabeth waved him off, turning her attention back to the screen, and he slipped out, heading for the locker room.

***

"I won't be long," he said quietly as he tugged on his boots.

"No?" Alice said noncommittally. She was standing by the door with her back to him, the way she always did in the locker room.

"No. Get in, drop the stuff off, come back." He tied the last lace, frowning. "You never told me what you think of the plan."

"I don't have an opinion."

"On the destruction of the Wraith?"

She turned to eye him. "You're not destroying the Wraith, John. You're just creating a food source to strengthen one faction. You don't suppose they'll change every Wraith, do you? They'll just pressure everyone into joining them. You're _uniting_ the factions, not destroying them."

John sat up, studying her. "That's a pretty depressing view."

"I fought the Wraith for hundreds of years, John. They are not capable of working for anyone's benefit but their own. Take the lifesigns detector with you."

"Always do. I'll see you later."

"Be safe, John."

"You too."

***

Radek yawned, promising himself a break in five minutes. The Wraith information was fascinating, but there was so much he knew he'd barely scratched the surface.

His screen flickered suddenly, _Danger Danger Danger_ scrolling across it in Czech before vanishing. He sat upright, blinking as the information began to disappear.

He glanced at the nearest desk. "Is your terminal...?" He cut himself off as every screen started flickering, information vanishing as he watched.

"You need to see this," one of the techs said, pushing a tablet into his hands. He stared at it, unable for a moment to comprehend what he was seeing.

"Oh no. Tell me the Daedalus has not left yet."

"Almost half an hour ago," she said apologetically.

"Shut everything down! Everything!" He dashed for the door, triggering his radio. "Dr Weir, we have a problem!"

***

"We got hacked," he explained to Elizabeth and the others a little later. "Within the hive ship's schematics was a worm-like computer virus."

"Your people went over the data," Elizabeth reminded him.

"I know. We thought it was clean, but this virus was entirely different."

"What did it do?"

"It very selectively probed our systems without damaging them or exposing itself."

"I don't understand," Carson protested. "If you didn't find it and it didn't reveal itself..."

"Once the hive left Atlantis, the worm began to destroy all the data they had sent down."

"Then this was their plan all along." In another woman, that would have been smug, but Teyla managed to sound only concerned.

"What did they get?" Elizabeth asked him.

Radek glanced automatically at the tablet in his hand. "This is one of the reasons we didn't detect it. They only uploaded two pieces of information: one – the Aurora mission reports..."

"OK," Elizabeth agreed. That could have been worse; Aurora had little sensitive information. "And two?"

He took a deep breath. "The location of every world on our database."

Elizabeth stared at him. "They have..."

"Location of Earth, yes."

"And there's no word from the Daedalus or our Hive?"

"Nothing. All sensors are searching."

"Alright. We need to warn Earth. Prepare to dial them up."

Radek nodded, heading out to the Control Room and carefully laying his tablet on the side of one of the panels. "Alice?" he said under his breath.

The tablet flickered. 'Systems critical, reboot necessary' scrolled across the screen, flickering in and out. Radek grimaced, taking a deep breath.

"Go offline," he murmured. "Rest and repair. Return to us when you are strong."

'Aid required?'

He laughed softly, ignoring the odd looks he was getting. "Yes. But repairs come first."

'Status of essential personnel?'

"Radek?"

Teyla was standing beside him when he looked up. "Is there a problem with the dial up?"

"No. No, dial up is ready to go on Dr Weir's command." Lowering his voice, he added, "Alice is injured and will not go offline until she has been told what is happening."

"I will inform Alice." She smiled, squeezing his shoulder. "Get some rest, Radek."

He nodded, glancing down at the tablet again as she walked away. "There is no response from the Daedalus yet, Alice, nor the Hive. We don't know the status of our personnel."

The screen stayed blank for several seconds, until he began to think she'd gone offline involuntarily; then the words 'Must remain online until all personnel are accounted for' appeared.

Radek didn't answer, watching the one sided replies as Alice spoke with Teyla. Finally she seemed to have talked the program down; the last message was 'Expected reboot time estimated at four hours thirty nine minutes.'

"Sleep well," Radek murmured in Czech, straightening up as Elizabeth stepped out of her office.

"Dr Zelenka, please dial Earth. We need to warn them that the Wraith are on their way."


	19. Misbegotten

3.02 Misbegotten

"Lorne!"

Lorne glanced over his shoulder, slowing as John caught up with him. "Sir."

"Got your team for _Orion_?"

"Yessir, we're just getting ready to leave now."

"You got Zelenka?"

"Zelenka," Lorne repeated. "No, he wanted to stay here and finish checking over the systems, make sure the Wraith worm didn't do any damage."

"Do me a favor and take him with you."

"Aye sir. Any particular reason?"

"_Orion_ has an operational AI. He's already working to speed up repairs, but with Zelenka along he'll be able to work even faster."

"An AI? What'd you name this one?"

"Ryan," John told him.

"Ryan from the Orion. Of course you did."

"That reminds me. Alice?"

Lorne leaned against the wall, watching. It was always fun watching John talk to Alice. Sort of like what he imagined McKay would be if he were invisible.

"I'm _Orion's_ captain, right?"

"Interim captain, yes," Alice agreed.

"Shouldn't I have the destruct codes, then?"

"Are you planning on blowing it up?"

Lorne snickered, turning it into a cough when John glared at him.

"No, Alice, I'm not planning on blowing it up."

Alice didn't answer, and he glared. "I'm still _your_ captain."

"I don't have the codes. Ryan has them."

"Why don't you have them? You're the fleet commander."

"No," she said patiently. "The codes were never stored in my memory. Security. The AIs hold them."

"Sir?" Lorne said carefully. "Aren't I going to be captain?"

"It's a position, not a title," Alice told him. "Captain is not always the commander. No, wait. It's a title, not a position."

Lorne glanced at John, who shrugged. "He is going to be in command, Alice. And he'll be able to hear Ryan if he needs to."

Alice was silent for a moment. "Yes. Then Ryan will give him the codes when he takes command."

"Are you talking to him right now?" John demanded. "I thought you had to be closer!"

"No. When did I say that? I can talk to Ryan at almost half a light year out."

"You couldn't talk to Rodney's 'Jumper when we were directly above it."

"Oh, 'Jumpers. That's different. They have little to no power. They don't need it. But I am the cityship, and _Orion_ is a ship of the line."

Lorne cleared his throat, smiling faintly when John looked up as though surprised. "I'll go find Zelenka, then."

"Ryan will give you the codes whenever you're alone," Alice told him. "And he knows he may communicate with Zelenka. Please take care of the ship, Evan."

"I will," Lorne promised. John nodded dismissal and he headed down towards the labs to find Zelenka.

***

"Woolsey's leaving," Alice said conversationally.

"Is he?" John didn't look up from his report. "What'd he decide?"

"That Elizabeth should remain as leader of the expedition, and her actions have been correct."

"Did your formality routines reset when you rebooted?"

"I don't have formality routines, John."

"Shame you missed all the excitement."

"Yes, fighting Hives and turning Wraith into men is just the kind of mission I enjoy."

"Tell me something."

"Yes, John?"

"Why do the 'Jumpers have Alices instead of Ryans?"

"I don't understand the question."

"The research stations and city ships have Alices, right?"

"Yes."

"And the warships have Ryans...AIs."

"Yes. The AIs have much greater control over the ship's functions than the research programs."

"Right. The 'Jumpers are ships. How come they have Alices?"

"Because they're not designed as warships, John. They're transports."

"With weapons."

Alice snorted. "Yes, a handful of drones. Do you want a Ryan program? The Alices can be upgraded on the Gateships if you want. They already have more control over the ships than I have over the City; it wouldn't be hard."

"No!" John paused, studying her. "Can you do that?"

"Yes, if you want. Elizabeth's coming."

"Here?"

His door chimed; Alice spread her hands, skipping out of John's way as he went to answer it. "Elizabeth! What a surprise."

"Am I interrupting?"

"No, of course not. Come in. Woolsey still here?"

"No, he's just returned to Earth." She glanced around the room absently. "He's recommended that I stay on as leader."

"Of course he has." John cleared a chair for her, dropping the folders onto his bed. "Never doubted it."

"Really?"

"Did you?"

"For a moment, yes. It seemed like everything we touched went wrong."

"Ah, we had a run of bad luck, that's all. It happens."

Elizabeth nodded, rising to her feet again. "Well, I just wanted to tell you you can stop reigning in that instinct to kill Woolsey. Until the next time."

John grinned, moving towards the door. "I'm quite proud of myself, actually."

"Yes, you did very well," Elizabeth agreed. "Of course, spending all that time on the Hive probably helped."

"I'd rather be on a Hive."

"Hmm." She left, smiling again.

"Woolsey wasn't that bad," Alice said thoughtfully.

John picked up his pen to start working on his report again. "He wasn't questioning your decisions."

"Yes, but the bulk of my decisions are actually your decisions, so he'd end up talking to you anyway."

"Yeah, good point." He sighed. "Tell me again why I'm writing this report on paper?"

"I really don't know, John. I'm afraid I can't help with it, either." She leaned over the desk from the other side, studying it. "Oh, you're spelt _Daedalus_ wrong right there."

"What would I do without you," John said flatly, scratching it out.

"Misspell your reports. And that would be a shame." Catching the look on his face, she added quickly, "I think I'll go and see how Zelenka's doing. He's very fond of _Orion_, after spending so much time saving her."

"That might be an idea," John agreed. _Orion_ had very nearly been destroyed in the battle despite everything Ryan and Zelenka had done, but she'd scraped through. Her engines were shot again, but Zelenka was confident they could get her up and running.

Alice smiled, vanishing, and he turned back to his report.


	20. The Return

I own nothing. Except the bits I own.

* * *

3.10 - THE RETURN

"Is Rodney's plan really going to work?"

Alice looked up from the screen. "His math works out."

"Yeah, but math isn't always all that counts."

"I can't see the future, John, but Rodney is right far more often than he's wrong, and this is a good plan."

"Yeah..."

"And Radek's double checked everything."

"Now we're talking."

"_John? _Daedalus_ is ready when you are,_" Elizabeth told him.

"Right," John agreed, powering up the 'Jumper. "Gate is dialed, forwarding macro has been updated."

Elizabeth was watching from the balcony; he tossed off a wave, and she smiled. "_Alright, John. You have a go._"

"Alright, then. Here goes."

He headed through the 'Gate.

The journey seemed longer than usual, but eventually he flew out on the other end. _Daedalus_ was hovering nearby.

"_Colonel Sheppard, right on time. What's your status?_" Caldwell asked.

"Felt a little weird, but everything seems to be in one piece. Ready to proceed to next phase. Uploading macro and initiating dialing sequence."

He dialed in the address, watching the 'Gate lit up. "Alice," he murmured, "stay out of sight on the other side."

"Yes, John."

The 'Gate connected, and he triggered the 'comm again. "_Daedalus_, ready to proceed."

There was a long pause before Caldwell came back on the line. "_Colonel Sheppard, you have a go._"

John took a deep breath, nudging the 'Jumper forward.

The 'Gate room in Cheyenne seemed smaller than he remembered; he drew the 'Jumper to a neat halt, just in front of the control room window. General O'Neill and General Landy were watching, both looking amused.

"_It's about time!_" O'Neill said over the comm.

"Sorry, sir," John said contritely.

"_Colonel Sheppard. Welcome to Earth,_" Landry said.

"Thank you, sir. Good to be back."

"_You know where to park. We'll debrief and go over the flight data as soon as you're ready._"

"Yes, sir."

He lifted the 'Jumper up towards the roof.

"He has the gene," Alice said from the back of the 'Jumper.

"Yeah, General O'Neill. I gotta go debrief; stay off line, alright?"

"Yes, John."

"And no poking around the SGC computers!"

"No, John."

He grinned, powering down the 'Jumper and heading out to meet the generals.

* * *

Debriefing over, he headed back through the 'Gate to test the procedure in reverse. _Daedalus_ was still standing by, hovering not far from the framework for the Midway Station.

"_Colonel Sheppard, welcome back to the middle of nowhere._"

"Thank you, Colonel. I've got a take-out pizza for everyone back at Atlantis. With your permission, I'd like to upload the macro and dial out before it gets cold."

"_Negative_," Caldwell said absently. "_We're putting that leg of the trip on hold for now. Seems like we're expecting company._"

"Company?"

"_Yeah. Come aboard, Dr McKay's just dying to tell you all about it."_

"Translation," Alice murmured. "He's already driven everyone else crazy talking about it, and now it's your turn."

"On my way," John acknowledged, flipping the comm. off and heading for the docking bay.

* * *

Rodney's plan to contact the strange ship, such as it was, was ready. John stood on the Bridge, watching the viewscreen.

"They're gonna fly by us in three, two, one."

The other ship was barely even visible before it was gone again. Rodney studied his screen, frowning. "Interesting."

"What?" Caldwell asked.

"If these readings are correct – and to be perfectly fair, they may not be ..."

"Rodney," John said warningly.

"It's an Ancient warship. It's possibly Aurora class."

"Who's flying it?" Caldwell protested.

"I ... would imagine Ancients."

"But there hasn't been any of them around for over ten thousand years."

"Relativity?" Rodney reminded him. "Look, remember, for them only a handful of years have passed."

"Don't those ships have hyperdrives?" John asked.

"Well, maybe their hyperdrive was damaged in a battle with the Wraith," Rodney suggested. "It happened to us all the time. Maybe it conked out on the way and they were forced to continue at as close to light speed as possible. That would explain how they got a million light years away from Pegasus without having to leave a million years ago."

"You know the subspace drive specs better than I do, Doctor, but I'm not sure an Aurora class ship has the power to do what you're suggesting." Caldwell frowned, studying the screen.

"Well, maybe they have a ZedPM."

John grinned. "That would be worth finding out."

"OK, we need to send them a message before they get out of range and we have to jump ahead. Uh, something like, you know, 'We are humans from Earth currently occupying Atlantis, uh, yada, yada, yada ...' "

"Why don't we just ask `em to slow down?" John suggested.

"Colonel Caldwell," Kleinman said from the helm. "The unidentified vessel is slowing down."

"Maybe they heard me," John said, shrugging.

"No, they saw us." Rodney leaned over Kleinman's shoulder. "They're not just slowing down – they're slamming on the brakes at something like twenty-seven gees."

"So now what?" Caldwell asked.

A hologram of a blond woman appeared at the front of the Bridge. John blinked, looking at her in surprise; she was wearing the Ancient uniform.

"Unknown vessel, I'm Captain Helia of the Lantean warship _Tria_. Our ship has suffered damage. We've scanned your vessel and determined that it is capable of hyperspace travel. We've begun deceleration maneuvers. Will you render assistance in the form of hyperspace transport?"

"Well, yes! Yes, of course we will," McKay said quickly.

Helia didn't react, watching them patiently.

"I don't think she can hear you," John said lightly.

Caldwell turned to Kleinman. "Open a channel. This is Colonel Steven Caldwell of the Earth ship _Daedalus_. It would be an honour to render assistance in any way we possibly can."

Helia smiled politely, bowing her head, and the hologram vanished.

"We're gonna meet Ancients!" Rodney laughed. "I mean, flesh and blood Ancients who know what everything is and how everything works! I mean, I don't even know what to ask first!"

"Well, it's gonna be a couple of hours before we can match velocities for transport," Caldwell told him.

"That should give you enough time to write out that list," John added.

"Right, right!" He hurried off, grinning.

John excused himself to Caldwell, heading for the docking bay and climbing into his 'Jumper. "Alice, how close to Atlantis do we need to be for you to talk to her?"

"A lot closer than this. Why?"

"We've met a ship called the _Tria_. Do you know it?"

"_Tria_ was assumed lost, shortly before the People left Atlantis. Captain Helia commanding. Why would she still be here?"

"Problem with her hyperdrive, apparently. Look, as soon as we get close enough to Atlantis, warn her."

"_Tria_ will be able to talk to Atlantis much sooner than I will."

"Do it anyway. Her engines are shot, she might be staying here. That'd give us a better chance."

Alice nodded slowly. "You know Alice will have to follow their orders above yours, unless they clash with her self-preservation order."

"Yeah, I know, but maybe we can get some warning this time, huh? Just give her the warning when you can."

"Yes, John."

* * *

Helia was polite but noncommittal when _Daedalus_ finally matched speeds. Caldwell transported her crew aboard and the ship started back towards Atlantis.

John and Rodney beamed down to the 'Gate room with Helia and a couple of her crew. Elizabeth was waiting, flanked by Teyla and Ronon.

"Doctor Weir, Ronon, Teyla – this is Helia, captain of the Ancient ship _Tria_." John glanced around; Alice was standing by the stairs, watching them warily.

"It's an honor to meet you," Elizabeth said.

"Thank you." Helia smiled, bowing her head. "And from what I'm told, you've done a remarkable job preserving our city."

"We did what we could with what we had."

"I need to speak to the leader of your people."

Elizabeth frowned, glancing at John. "I'm in charge of the Atlantis expedition."

"You misunderstand me, Doctor Weir. I need to talk to the one who can speak for _all_ the people of Earth."

"That can certainly be arranged, but may I ask why?"

Helia looked away. A small console lifted up from the floor between them; John and the others all took a step back, Ronon drawing his blaster.

"What is that?" Rodney demanded. "How come I've never seen that?"

Helia laid her hand on the console and every screen in the control room turned off. Alice flinched, taking a step forward before catching herself to stand still.

"Excuse me, what's going on?" Elizabeth asked.

"Thank you for all that you've done, Doctor Weir, but your guardianship of this city is no longer necessary. The city is now under my control." Helia smiled politely.

"Your cont...I'm sorry, but that is not..."

"We wish to speak to your leader," Helia interrupted her. "Please arrange this. We have no wish to harm you or any of your people, Dr Weir. As I've said, we are truly grateful for everything you've done here."

"Captain Helia," Alice said carefully.

"Later," Helia told her. "Dr Weir, please arrange the conversation."

"John, I would," Alice advised him. "Captain Helia commands the _Tria_ for a reason."

"Yeah. Elizabeth, let's go call home, huh?" To Helia, he added, "We need to dial the 'Gate."

"Of course." She touched the console again.

"We have 'Gate control!" someone called from the balcony.

"Elizabeth," John repeated, touching her elbow. "Come on."

Elizabeth let him draw her away, scowling. "John..."

"We don't have a choice," he murmured. "They can turn Atlantis against us. Let's just call Earth right now, alright?"

"They can't do this," Elizabeth said quietly, but she followed him to the Control room anyway.

* * *

Being kept out of meetings wasn't as much fun anymore, John decided. Helia was more or less ignoring Alice, but her programming still kept her from disobeying even the implied orders and she was having trouble keeping him as up to date as usual.

Richard Woolsey, from the IOA, and General O'Neill had come to meet with Helia in the hopes of changing her mind. It didn't seem to be going very well.

"Helia won't change her decision," Alice said now, glancing nervously over her shoulder. "Your men have made some good arguments, but she won't listen."

"You're right. They want us out of here." John glanced up, catching Elizabeth's eye.

"But why?" Rodney protested. "There are maybe a hundred of so of them? I mean, they could use us. They might even _need_ us."

"What if you were forced from your home by a war, only to return to find someone on _your_ couch, eating _your_ Cheetos, watching _your_ TV?" John raised an eyebrow at him.

"Well, I'd be fine with that," Rodney muttered, but he wasn't fooling anyone.

"No, you wouldn't."

Alice vanished as Jack and Woolsey came in. John rose to his feet, watching them.

"How go the talks, sir?"

"No talks," Jack said ruefully. "Listening is what we did."

"It was essentially a transitional meeting," Woolsey agreed. "They needed to know how much time we needed to vacate the city."

"I said forty-eight hours, unless you need more." Jack looked at Elizabeth.

"No. It should be enough." She turned away, staring at the wall.

"That's it? We're just gonna take this lying down? We rescued them!" Rodney looked from one to another of them.

"And they're immensely grateful," Woolsey agreed.

"Well, they're not showing it!"

"From their point of view, Doctor McKay, they're being extremely generous. Keep in mind that when they left Atlantis, we were basically a hunter-gatherer species."

"Well, did you remind them that if we hadn't hunted and gathered them out of the void between galaxies, they would still be stuck there?"

"We should have left them out there," John muttered.

"I know you feel as though you're losing the city," Woolsey started.

"This isn't just about losing a city, Richard," Elizabeth said sharply. "It's about losing an opportunity to talk with and learn from living, breathing Ancients."

"They are willing, over time, to let us back in the city – just not right now. That way we get all the benefit of Atlantis with very little of the risks ... or expense."

"Yeah, it's not like we don't have our own galaxy to worry about," Jack agreed.

John grimaced, leaning back against the wall. Rodney had given up as well – he could read it in the slump of his shoulders.

"Colonel, I'd like you to supervise the withdrawal," Jack said gently.

John glanced at Elizabeth before nodding. "Yes, sir. What about _Orion_?"

"_Orion's_ on New Taranis at the moment," Elizabeth reminded him. "She can stay there. Helia doesn't seem to know or care about any of the other ships."

"Go ahead," Jack said quietly. John and Rodney headed out with Woolsey to start the evacuation.

"They want Woolsey to stay," Alice said abruptly, stepping out of a doorway to join them. A passing Ancient glanced at them, frowning; Alice didn't react except to nod slightly. "An ambassador, O'Neill says."

John nodded, turning away to go and find Lorne and get the Marines moving.

* * *

Late that night John stood outside Elizabeth's quarters, scribbling on a notepad. They were almost ready to leave; he'd been putting off this conversation for most of the evening, now.

"John?" Alice said quietly.

"Yeah."

"I'm sorry you're leaving."

He glanced up from his notebook. "Yeah. I'm sorry we're leaving, too. Helia gonna keep you around?"

"She hasn't said. She hasn't really seen me yet. None of them have."

John nodded, remembering a 'Jumper on Proculus and Alice sounding very young as she said '_I'm made to be useful. Without you I can't fulfill my function. I want to be useful_.' "They're still settling back in. I'm sure they'll have all kinds of research for you, once they get going."

"Yes, I'm sure they will."

"Elizabeth still up?"

"Yes, she's awake."

"Thanks."

Alice nodded, turning away, and he said quickly, "Hey. Thanks. I mean it."

"You're welcome, John."

He let her go, turning to tap the chime on Elizabeth's door.

* * *

Rodney was still subtly trying to get Helia to let them stay. Since his campaign was mostly pointing out things that had gone wrong since the City had risen, it wasn't working very well.

"Rodney!" Elizabeth called.

He leaned over the railing, grimacing. "Uh, right, yes, well. I gotta go."

Helia smiled faintly as he turned away, not quite hiding her relief.

"You have been good friends," Teyla said. "To all the people of this galaxy."

John took a step closer to her, bowing his head. She matched his move, resting her forehead against his.

"Farewell," she murmured.

"Take care," John said, just as softly.

"Bye." Rodney waved, ducking past them to join Carson and Elizabeth.

John looked past her to Alice, standing at the base of the stairs. "Be careful," he said, looking back at Teyla.

"We shall."

Elizabeth led them towards the 'Gate, pausing just before she stepped across the horizon to look back. John didn't, pushing forward and leaving the City behind.

* * *

Seeing Atlantis on a screen, John decided six weeks later, was worse than never seeing it again. General O'Neill had returned to Atlantis to help Woolsey with his liasing. It wasn't going very well, apparently.

"General!" Jack said cheerfully.

"General!" Landry echoed.

"Is that Sheppard there with you?"

"Yes, sir," John said in surprise.

"Oh, good. Tell me, Sheppard, did you leave me anything? Any little helpful thing?"

"Helpful...?"

"Yay high, kinda hard to understand?" He gestured vaguely; Woolsey was frowning at him, but he ignored the look.

"...thing," John finished, suddenly understanding. "Yes, I did leave that helpful thing. How's it working out?"

"Little quirky!"

"Yeah, you get used to that. I just thought it might come in handy for you. Strange city and all that."

"No..." Jack said thoughtfully. "Yes. It is helpful. Thank you."

"My pleasure, sir."

"Are you done?" Woolsey demanded.

"Not sure. You watch the Simpsons at all, Sheppard?"

"Sorry, sir, I was off world on Sunday."

"Aw, shucks." He turned to Woolsey. "We're done now."

"Thank you."

"No, thank _you_."

Landry was chuckling quietly, but he stopped when Woolsey started talking.

"Talks are proceeding at an acceptable pace; but the real news is that the Pegasus Replicators are heading back to Atlantis to make another run at the city."

"They are?" John said in surprise.

"No-one here seems to be that worried about it." Jack shrugged.

"Why not?" Landry asked.

"They're Ancients!"

"Apparently these Replicators have a law in their base code that makes it impossible for them to harm their creators," Woolsey said. Jack was frowning slightly; Alice must have been talking to him, John realized.

"And they're expecting to find us," John realized.

"According to Helia, they're gonna run into some kinda nasty surprise," Jack said.

"So you can pass it on to Doctor McKay that if you and he hadn't rescued the Ancients and returned Atlantis to their care ..."

"... I'd have lost the city anyway," John finished when Woolsey trailed off.

"Right," Jack agreed. "Well, we should get back to our talks...and talks and talks. O'Neill out."

John turned to Landry as the 'Gate shut down. "Sir, I'd be happy to talk to you more about these Replicator guys."

"Naah, sounds like they've got everything under control. Assuming Jack can handle whatever secret 'thing' you left for him." He was grinning, so John didn't think he was that upset.

"Yes, sir."

* * *

A day or two later Jack stood in the Control room on Atlantis, watching the screen as it displayed the oncoming Hive. A 'Jumper had launched and was approaching it.

"That seems like a pretty big ship," Woolsey said nervously. "You're sure only sending one Jumper up to fend it off is the right thing to do?"

"It is impossible for them to harm us," Helia reminded him patiently. She did a lot of things patiently; it was like being surrounded by teachers.

"I could use some enemies like that," Jack murmured.

"_We have established communications, Commander_," the 'Jumper pilot told them.

"This is Commander Helia. The city you're approaching is once again under Lantean control. Stand down and return to your planet immediately, or you will be ..."

The tiny ship disappeared.

"They destroyed it!" Alice was suddenly beside Jack, staring wide eyed at the screen.

"I thought you said they couldn't harm you!" Woolsey protested.

Helia ignored him, turning to one of her crew. "Raise the shield!"

The shield started to raise but before it could fully cover the City an explosion rocked the room. Several panels exploded, sending sparks raining through the air.

"General!" Alice called from a corridor. Jack glanced around; Helia was already trying to coordinate retaliation, but she spared a moment to wave him off.

"Come on." He caught Woolsey's arm, hauling him into the corridor. "Where are we going?"

"You're asking me?" Woolsey protested.

"No. Shush. Where are we going?"

"Comm station," Alice told him. "Commander Helia is preparing to dial Earth. You need to request backup."

"She's asking for backup?"

Woolsey squinted. "Who is?"

"Shh," Jack said irritably.

"She has no choice. They can't defeat the Replicators; the code was their only defence. Your people have weapons proven effective against the Replicators."

"Oh, now they want our help?"

"General, who are you talking to?" Woolsey protested.

"Atlantis' AI."

"I'm not an AI," Alice reminded him.

"He doesn't need all the words, they'll just confuse him." To Wolsey, he added, "Atlantis has an AI – type thing – and she's trying to help us. Helia's going to dial Earth, and we need to send a request for help. Got it? Which way?"

"Here." Alice was standing by a ladder to the lower levels. "Transporters are out. You need to run."

"Running it is," Jack said with a sigh.

_

* * *

"Atlantis is under attack from Replicators. Somehow they figured out how to override their programming. The Ancients were taken off guard and have lost most of the city already. Request immediate evacuation!"_

"_They're coming!"_

General Landry clicked off the screen, turning back to the table. Elizabeth, John and Rodney, and Carson were watching in disbelief.

"They never made it to the 'Gate. I was informed they had a law written into their base code that made it impossible for them to harm the Ancients. How the hell did this happen?"

"It is remotely possible that in trying to rewrite Niam's base code, I ... uh, we may have opened the door for them to make other changes." Rodney winced.

"_You_ did this?"

"At the time we thought it was the only possible way to save the city," Elizabeth reminded him.

"How it happened doesn't matter," John pointed out. "They may have changed it on their own. The question is: how do we fix it?"

"That's why I called you in. I have my orders." To give him credit, Landry looked faintly upset. "The _Daedalus_ is already on the way. Now, what I need from you is ... what's the best way to get a nuke past the shield?"

* * *

Late that night John and the others slipped into the temporary 'Jumper bay. John moved around to the front of the 'Jumper, peering through the windshield. Alice was standing in the cabin door with her back to him, watching Sergeant Siler fiddle with something. She turned abruptly to look at him, grinning; he ducked out of sight, edging around to the back. Leaning around the edge of the hatch he triggered his zat; Siler collapsed, rolling down the ramp to land in a heap on the floor.

"Let's move!" John ordered, scrambling into the 'Jumper. Carson hunkered beside Siler, checking him over quickly before climbing in after the others. Rodney dialed the 'Gate quickly.

"You set?"

"Go for it," John agreed, settling into the pilot's seat. The preflight was all done and he started them going immediately.

"OK, they'll be able to get through my hack pretty quickly," Rodney warned him, dropping into the seat beside him.

"It's alright – I don't need much time." The 'Jumper was already dropping through the ceiling of the 'Gate room, rotating to face the 'Gate.

The radio flicked on. "Colonel Sheppard, stand down! That is a direct order!"

They were through the 'Gate before the sentence had finished. John flipped the radio off as they arrived at the Midway Station.

Rodney turned to the console behind John, working quickly.

"My turtles!" Carson blurted.

"What?" Elizabeth asked.

"I just bought some wee baby turtles and no-one knows to feed them."

"Well, turtles are pretty hardy," she said uncertainly. "I'm sure they'll be fine."

"And they make good soup," John muttered.

"I figured I'm back for good so I might as well get a pet. I'm allergic to cats and, well, I'm at work too long to be fair to a dog, so I went with turtles. I've probably killed them."

"Any time now, McKay!" John snapped.

"Oh, trust me, I am going as fast as I can!"

"Poor little buggers." Carson shook his head.

The HUD flashed up; John turned around, frowning at it. "The Milky Way 'Gate just activated. Did you do that?"

The HUD vanished and Landry's face appeared. Rodney leaned back in his seat, eyeing it. "Nope."

_"Colonel Sheppard. I'm going to assume that you're still at the midway station waiting for Doctor McKay to rewrite his macro. I understand what you're doing, Colonel. Hell, I'll even call it brave. But if you don't turn that ship around immediately and come back to the SGC, I'll see to it personally that your career in the military is ..."_

John cut it off before he could finish the sentence. "That way I won't know what he was gonna say," he explained when Elizabeth stared at him.

"OK. OK, I've got it," Rodney announced.

"Alright. Last chance to change our minds."

No one spoke, and he nodded quickly. "Alright. Let's do it."

They plunged through the wormhole.

* * *

The 'Jumper came through a 'Gate on the new Athosian homeworld. John switched on the cloak, busying himself with the final checks while the others filed out.

"Welcome home," Alice murmured.

"Thanks. Can you find Teyla and Ronon from here?"

The HUD flashed up and he studied it for a moment, watching the two blinking life signs. "Good."

"Do you have a plan, John?"

"Yeah. I have a plan. We'll be back in a little while...hopefully with Teyla and Ronon."

"John!" Elizabeth called from outside. "Ready?"

"Coming!" He flicked the HUD off again, heading out of the 'Jumper.

* * *

The preflight had been done again when they got back to the 'Jumper. John smiled quickly at Alice, dropping into the pilot's seat and bringing everything online. "McKay?"

"Give me a second, we just got here...OK, I think I've loaded up the GDO. It'll lower the shield when we dial."

"Go for it."

"Alright. Dialing Atlantis." The 'Gate dialed out and he studied his laptop for a moment. "That's confirmation. The 'Gate shield has been lowered."

"I hope this little plan of ours works."

"Ah, you and me both."

They entered the wormhole.


	21. The Return pt 2

THE RETURN

"Tell me again what you are," Jack said quietly.

"I am a representation of the scanners and memory banks, designed to facilitate information gathering," Alice said patiently. "For security reasons I can only be perceived by those with what you call the ATA gene naturally, and even then only with a certain proficiency."

"Yeah, all I'm hearing is blah, blah, blah."

"I'm the city's brain," she said slowly.

"Ok. That, I understood. Why are you helping me?"

"John Sheppard is my captain. You are his captain. My loyalty is with you, not with the Asurans. They're much farther from the People than you are." She looked past him. "Your companion is not very happy."

"Woolsey? Yeah, he's not really used to this kind of thing."

"General?" Woolsey hissed from the next corridor.

"See, that's just not the sort of thing you do when you're hiding."

"No one's here," Alice told him. "No Asurans anywhere near here."

"You're sure? No Replibugs creepy-crawling around anywhere?"

"No...Replibugs. You and he are the only lifesigns on this level."

"General?" Woolsey called again, louder.

Jack sighed, swinging around the corner to confront him. "And if I'm a Replicator?"

"Then I just exposed my position," Woolsey muttered.

"_Again_."

"I'm sorry. I'm not very good at this."

Jack tossed him an energy bar. "Here."

"Thank God! I'm starving! Is this all you could find?"

"No – actually there was a lovely buffet."

Woolsey was too busy eating the bar to roll his eyes, but he managed to give the impression that he had. "How did the recon go?"

Jack sat down. "Well, the Stargate Ops is crawlin' with `em. There's no way we're gonna get across to the Jumper Bay."

"Are they looking for us?" Woolsey finished the bar, stuffing the paper into his pocket.

"I plum forgot to ask," Jack told him.

"Not actively," Alice told him. "Though they will capture you if they see you, of course."

"Well, as long as the life signs detectors aren't working in these damaged areas, we should be able to hold out until they rescue us," Woolsey murmured.

"Uh, Richard, there's not going to _be_ a rescue."

"What?"

"Landry has standing orders to nuke the city if there's any sign of a foothold situation."

"What kind of a standing order is that?!" Woolsey demanded.

"Mine," Jack muttered.

Alice, still standing at the head of the corridor, looked up sharply. "You ordered the destruction of the city?"

"You'd rather the Replicators got their hands on her?" Jack asked.

"What are...oh." Woolsey scowled, playing with the wrapper from his bar. "The AI."

"_Alice,_" she said firmly.

"He can't hear you," Jack reminded her.

"That's no reason to be rude. I'm using his name."

"Uh, no, you're not."

"Well, I will if he will."

"I have a question," Woolsey said carefully. "If the scanners aren't working down here, how does the AI know where we are?"

"Alice," Jack told him.

"How does Alice know where we are," Woolsey rattled off.

Jack glanced up at Alice. "Care to explain?"

"Radek inserted a new level of scanners. The output's buried under seven different databases, and the power consumption's hidden as well. He's got them active in most of the City. He's been working on it for months."

"Promotion," Jack said in relief, summarizing quickly for Woolsey.

" 'Gate's open," Alice said suddenly, looking away.

Jack's radio beeped. "_Authentication code Alpha Six Delta Charlie Niner. General O'Neill, Woolsey – do you copy?_"

"Sheppard? Is that you?" Jack said in surprise.

"_Yes, sir. I need to know if you're anywhere near Stargate Operations._"

"No, we're not."

"_That's good. Can't talk right now, sir. I'll get back to you in a couple of hours. Sheppard out._"

"Can't talk right...Sheppard!"

An explosion rocked them; Jack caught the wall, frowning. Alice was staring upwards, expression totally blank.

"That sounded like an explosion," Woolsey said blankly.

"Because it _was_," Jack said absently.

"Is Sheppard attacking the city?"

"He'd _better_ be."

"He's just blown up the Control Centre. The whole tower." Alice vanished abruptly.

"Why can't he get back to us for two hours?" Woolsey asked.

"I don't know," Jack said semi patiently. "Alice!"

"He _blew up the central tower_," Alice said angrily from behind him.

"Did he tell you his plan?"

"No. Something to do with the Replicator they spaced a few months ago."

"They want to bring in _more_ Replicators?"

"He won't talk to Alice in the 'Jumper, and they're not talking about the plan. I don't know what the plan is."

"Keep an ear out, huh?"

Alice saluted absently, vanishing again.

***

John ignored the discussion coming from the back of the 'Jumper, watching the HUD carefully. "How close are we?" he muttered.

"You haven't told me what we're looking for, John," Alice said patiently.

"Niam."

"Oh. Then we are quite close. Perhaps another five minutes."

Teyla's voice was louder than the others when she spoke. "Should we not have informed General O'Neill of our plan?"

"He knows we're here," John said absently. "We'll contact him again as soon as we get closer to the city."

Rodney snorted. "Well, that is gonna be easier said than done. With all those hits we took, it's gonna be impossible for me to convert the shield back to a cloak."

"And by "impossible", you mean ..."

"I mean "not possible". What do you think I mean?"

"Well, hopefully we took out the sensors when we blew the tower," John said with a shrug.

"Alice isn't happy about that," Alice warned him.

"Well, you said they could rebuild remarkably fast," Elizabeth reminded Rodney. "How long before they restore critical systems?"

"A couple of hours?" he guessed.

"Plus the painting and redecorating," John added.

"If we time this right, this could work to our advantage."

"There," Alice said suddenly, pointing. The HUD flashed at the same time and John nodded.

"Got him. Right where we left him!"

"That's him," Rodney agreed.

"Who else would it be?" Ronon pointed out.

"True," Rodney said absently. "His power levels are barely registering. It's no wonder the Replicators didn't find him."

"Alright, I'll swing around and pick him up," John said. "Watch yourselves – I'm closing the bulkhead."

The group pulled forward into the cabin as the bulkhead closed.

"Will we not be vulnerable to the same nanovirus with which Niam infected Elizabeth?" Teyla asked.

"He's been floating in space for over a month now," Carson told her. "Existing in such a harsh environment, direct solar radiation has severely diminished his power levels. We're fairly certain he's almost completely incapacitated."

"Is he dead?" Ronon asked impatiently.

"As in 'mostly dead'. Besides, we don't have a choice. He's the key to our whole plan." Rodney didn't look up from his computer.

"Alright," Elizabeth agreed. "But if he even twitches..."

Ronon tapped his two ARG together. "Don't worry."

"Please make him stop doing that," Alice murmured. "He'll blow a hole in my wall if he's not careful."

John waved her off. "Got him. Closing the rear hatch. Take the seat," he added to Carson.

The doctor climbed into the pilot's seat as John headed towards the bulkhead door. He took one of the ARGs from Ronon; Ronon scowled, pulling out his own gun instead.

"The compartment's re-pressurised," Carson told them.

Ronon opened the door, aiming both weapons. John ducked around the door as it opened, moving out of Ronon's line of fire. Alice was crouched over Niam, frozen on his back.

"OK, OK, OK," Rodney murmured, coming into the compartment. Alice skipped out of his way, perching on the seat and watching him scan Niam.

"OK. This is good. His power levels are minimal but not *too* minimal. I'm fairly sure he doesn't have the juice to regain consciousness..."

"Careful," Alice said warningly. Rodney scrambled to his feet at the same time, backing away as Niam's hand twitched.

"Whoa..."

The movement faded. Ronon relaxed; Rodney leaned forward, peering at him. "I was ... fairly sure."

"Just load the programme," John ordered.

Rodney knelt down, typing slowly, glancing warily at Niam as he worked.

"Rodney has the best ideas," Alice said thoughtfully.

"He'll be thrilled that you think so," John muttered, powering the engines back up.

"Of _course_ I remember the plan. It's my plan," Rodney said from the back.

"Uh, actually, using Niam was Elizabeth's plan," John called back.

"Thank you!" Elizabeth said brightly.

"It was _mostly_ my plan," Rodney protested.

"Modest," Alice noted.

"You're figuring this out now? Where've you been for the past two years?"

Alice made a face at him, leaning against the helm and watching the argument in the back compartment.

"How _much_ closer?" Teyla was asking.

"_Much_," Rodney said impatiently.

"With no cloak?" Ronon asked.

"No cloak," Rodney agreed.

"Good to be back home, huh?" John said over his shoulder.

"Hmm! There's no place like it." Elizabeth came to join him, watching over his shoulder as they headed back towards Lantea.

***

Jack had found a ball somewhere in a pocket and was bouncing it off one of the walls. The steady beat had lulled Woolsey into a doze; Alice was watching closely, tracking the ball as it bounced.

"The Ancients must have played with balls," Jack said idly.

"Children's toys. For backwards children. No adult would ever…"

"Ever what?" He glanced up when she trailed off.

"We're firing drones."

"At what?"

"Jumper." She took a couple of steps away, looking upwards. "What's he…"

"What's happening?" Jack nudged Woolsey, waking him.

"Ow. John's flying them into my buildings." She scowled. "He knows better than that."

"That sounded like another explosion," Woolsey said worriedly.

"Yes. Yes, it did," Jack agreed.

"What does that mean?"

"Something exploded."

"But is it Sheppard attacking the Replicators, or the Replicators attacking Sheppard?"

"We'll find out!"

"How did they even get here? Through the Gate?"

"I've been sitting next to you through the whole thing," Jack pointed out. "Why do you think I have more information?"

"Look, I _told_ you I wasn't good at this. Can you just ask the AI…"

"Alice," Jack and Alice said at the same time.

"…what's going on?"

"He said he'd be back in a couple of hours," Jack reminded him, glancing at his watch. "That gives him a good ... eleven seconds."

Something very large exploded very near; Alice flickered, vanishing. Woolsey scrambled to his feet, clinging to the nearest steady piece of furniture. "What was that?"

Jack stood, glancing around. "Alice?...she's gone somewhere. Don't look at me like that, Woolsey, I have no idea what's going on."

***

"If we keep this up, there won't be much of a city left to save," Elizabeth said mildly.

"I'll try to run the drones into your least favorite buildings," John said absently. "McKay!"

"It should be working," Rodney protested.

"Jack and Woolsey are fine," Alice offered.

"Not the time!" he hissed, jerking the 'Jumper around another building. One of the pursuing drones clipped the rear shields.

"Shields have been damaged," Teyla said calmly.

"Alright, I've had enough. I've got a different idea." John took them out of the City.

"I hate this idea," Alice muttered. John grinned, retracting the drive pods and taking them under the water. The drones lost sight of them, heading upwards instead.

***

"They're overdue," Woolsey said impatiently.

"Not yet."

"It's been _well_ over eleven seconds."

"Yes. But you've been ignoring the dramatic element of ..."

He trailed off as Alice reappeared, glancing around in something like confusion. Catching Woolsey's look, he added absently, "... suspense."

"_General O'Neill. Are you there, sir?"_

"They're fine," Alice said belatedly.

"See?" Jack told Woolsey. "Yes, we're here. You're late."

"_Sorry, sir. Had to go into space and pick up some ...frozen goods._"

"He's got a Replicator in the 'Jumper," Alice added.

"Whatever. Where are you now?"

"_We're not exactly inside the city yet. We're headed toward an underwater Jumper Bay._"

"_Well, what we think _may _be an underwater Jumper Bay,_" Elizabeth qualified.

"Is that Doctor Weir I hear?" Jack asked.

"_Yes, General. It's good to hear your voice too."_

"I didn't say it was _good_, Elizabeth. Please, don't be offended as I express my ... _surprise_ that Landry would send you on a mission like this."

Elizabeth hesitated. "_Well, sir, General Landry didn't sanction this mission._"

"So, am I to assume you are _not_ surrounded by heavily-armed SG teams and young strapping marines?"

"In one 'Jumper?" Alice pointed out. "You know how big they are, right?"

"_You've got Colonel Sheppard, Ronon, Teyla, McKay, myself and Doctor Beckett._"

"Ooh! Doctor Beckett, is it? Well, _I'm_ comforted."

"Hey, stop that. Carson's good people," Alice said sharply. Jack scowled at her, but John was already speaking.

"_We've got a plan, sir, a good one._"

"Yes, Colonel, I'm sure you do," Jack agreed. "But in the unlikely event you don't fail miserably, you're fired."

"_Yes, sir. Look…forward to that._"

"They have a plan," Jack told Woolsey, flicking the radio off.

"I heard." Woolsey didn't sound any more reassured than Jack did.

"It's a good plan," Alice offered.

"Yeah, but you thought sending one 'Jumper to meet the Replicators was a good plan," Jack pointed out.

"No I didn't. No one asked me. I'd have _told_ them it was a stupid idea." She glanced down suddenly. "Trouble."

***

"Careful," Carson murmured, wincing as John steered the 'Jumper through the entrance to the bay.

"Thanks, Doc!" John gritted. The 'Jumper felt three times as heavy and moved much more sluggishly than he was used to.

"OK," Rodney said once they'd landed. "Closing the outer door. Yes. Now, I just have to pressurize the compartment and we are ... Huh?"

"What?" John demanded.

"It's not letting me do it," Rodney said, bewildered.

"The water's not draining out," Carson noted.

"Yeah, excellent observation, thank you."

"It _is_, however, draining in," Elizabeth said from the rear compartment.

"Oh, not again," Rodney groaned.

John came back to examine the tiny crack. "Well, guess we took some damage."

"I just wanna point out that this was _not_ my idea," Rodney said flatly.

"You said, "Get us close to the city." This is pretty damned close!"

"And yet, no cigar!"

"Alright," John said, sighing. "Just open up the outer doors – I'll figure something else out."

"Right," Rodney agreed.

"That might be a problem," Alice murmured. John shooed Carson out of the pilot's seat, ignoring her.

"Ohhhh ... dear," Rodney said reluctantly.

"What?" Elizabeth demanded.

"I don't think I'm gonna be able to open the outer door."

"Why not?"

"I think it might be jammed."

" 'Might'?" John repeated.

"OK, 'is'."

"Well, that's unfortunate."

"Yeah, I'd have to agree with you on that."

"This part of the plan isn't going so well."

Alice laughed softly. "I think Elizabeth's about to hit you." She considered for a moment. "Ronon might hold you down for her. Do you two plan that?"

"Naturally gifted," he muttered.

"There must be a manual override somewhere," Elizabeth said thoughtfully.

"In the Bay's Control Room, yes," Rodney agreed.

"OK, I'll swim to it," John suggested, giving up on sealing the leak.

"... which is sealed from the other side," Rodney continued.

"Of _course_ it is!"

"It's a safety precaution," Alice muttered. She was sitting crosslegged on the bench seat, avoiding the deepening water.

"Perhaps General O'Neill can reach it," Teyla suggested.

"Good," Rodney agreed. "OK, give me half an hour to get Niam to the right power level so we can do this."

"We've got more than one fracture," John pointed out. "We don't have that kind of time." He touched his radio. "General O'Neill? We're gonna need a favor."

***

"_OK, there should be a hatch leading down to the next level. Do you see it?_"

"Yep. Sure do. We see it."

"_The Control Room should be almost directly below,_" Rodney continued, ignoring the sarcasm.

Jack glanced down into the hatch, sighing. "OK, slight problem here."

"_What's that?_"

"Well, the level below is completely flooded too."

"_Ah_." Rodney paused. "_I, uh, couldn't convince you to take a swim today, could I?_"

Jack winced, eyeing the water, and looked up at Alice. "Really?"

"They are not in danger yet, but soon. There is no other way…you'll have to swim sooner or later."

"Alright," he agreed reluctantly, passing the radio and his rifle to Woolsey. "If you hear something, don't call out to it. Shoot it."

"Understood."

"Anything that's not me is a Replicator, so don't hesitate." He kicked off his boots and pulled his jacket off, grimacing at the sight of the water.

"You won't be gone long, will you?" Woolsey asked.

"Uh, kinda depends on the temperature of the water." He tested it, shuddering. "Not long. McKay? What do I do once I get down there?"

"_It's a manual override. It should be in the centre of the console. It'll be obvious once you get in there._"

"Alright."

"Good luck," Woolsey offered.

"Thank you." He left the radio on the railing, climbing down the ladder. "Alright, here we go."

He could see the 'Jumper from the control room, though he couldn't make out any forms through the distortion of the water. The control panel had five sides and, despite Rodney's words, nothing particularly stood out. He poked half heartedly at a couple of controls before heading back to the ladder.

Woolsey was lying on the deck, peering into the water. Jack surfaced, blowing air out explosively.

"Did you do it?" Woolsey asked worriedly.

"Radio," Jack gasped. Woolsey pulled the radio off the railing, passing it down to him. "McKay?"

"_Did you do it?_" Rodney demanded.

"You and I have very different ideas of what "obvious" is."

"_Well, I've never seen it before!_"

"There are _dozens_ of controls down there I wouldn't even know how to describe." Jack scrubbed a hand through his hair.

"_Well, it's an emergency control,_" Rodney said. "_It should be among the most prominent._"

Jack turned the radio off, tossing it back to Woolsey. "You planning on helping?" he demanded.

"I've been try…"

"Not you!"

Woolsey grimaced, looking away. "The AI."

"Alice."

She looked up as though startled. "Yes?"

Jack rolled his eyes. "Show me the control!"

"Yes," she agreed.

"God," O'Neill muttered, pushing off again.

Alice was standing next to the console when he made it back into the room. Her hair wasn't moving in the water and she wasn't making any effort to stay in place. Jack groaned, following her pointing hand to one of the controls.

Through the window he could see the water starting to drain out of the bay. He let go, heading back for the door.

The lever popped back up and the water stopped draining. He glanced at it, torn, but his air was gone and he headed back for the ladder.

McKay was already complaining over the radio before he was even out of the water. "_It sounded like you had the right control. Why did you stop?_"

"It's a dead man's switch," Jack said wearily. "I have to hold it in place."

"_I had no idea._"

"Really? Nor did anyone here, apparently." He turned the radio off, glaring at Alice. "You couldn't have warned me?"

"Warned you?" she said blankly.

"About the…you know, never mind. Go find out what the Replicators are doing, alright?"

"I don't have to go anywhere…"

"Go. Away."

He dove without waiting for her answer, heading straight for the control and holding it down determinedly.

***

John caught the ARG Ronon pitched at him, checking it absently.

"Woolsey? ... Woolsey, come in," Rodney said for the fourth time.

"Something's wrong," John decided, triggering the hatch. "McKay – you stay here and reprogramme Niam. We're gonna go and meet General O'Neill and Woolsey, alright? We'll wait for your OK."

Rodney waved them off, turning back to his work, and John led Ronon, Elizabeth and Teyla out.

They found the hatch easily enough; it was still open, and the floor around it was covered in bullet casings. John crossed to look down the hatch.

"They have been captured?" Teyla asked, glancing around.

"Yeah, looks like," John agreed absently.

"Which means their minds will be probed for information any minute now," Elizabeth murmured.

John moved to check the far end of the corridor. Alice was standing just around the corner, staring towards the 'Jumper bay.

"Where are they?" he murmured.

"In the Brig," she said absently.

"Injured?"

"Your General isn't. It's hard to tell with the other one. He complains all the time."

"Yeah, he'll do that." Tapping his radio, he added, "McKay. Fire up that virus."

"_I am working as fast as I can,_" Rodney snapped.

He turned back towards the others. "The Replicators have O'Neill and Woolsey."

"_Unfortunately, that information can't make me work any faster._"

"This way," John told the others, flicking his radio off again.

***

Niam's inadvertent destruction meant the plan had to change, fast. Surprisingly it was Rodney who came up with it, including the double-bluff to keep the Replicators from figuring it out.

John stayed to lock down the 'Jumper, waiting until the others were gone to say, "Alice? You tell Big Sister about the plan?"

"No. Do you want me to?"

"Yeah, but tell her not to tell General O'Neill about it. In fact, tell her to stay out of the brig altogether."

"Yes, John." She glanced at the front viewscreen. "She doesn't like the plan."

"Too bad. We'll fix it later."

"Sheppard!" Rodney yelled from outside. "We have to move, we're on a schedule here!"

"Tell her to stay out of the brig," he repeated, snatching up his ARG and heading out to join Rodney.

***

There was no sign of Alice as they worked on the emitters; John kept an eye out, but Rodney was sticking too close for him to risk calling her. The timing was too close for him to risk dropping behind, and he gave up looking for her somewhere between emitters.

Apparently the Asurans had a sense of irony. No one was captured until they'd finished their work. John was quietly relieved about that; he'd worried that they'd be stopped before completing the reprogramming.

Instead the shield went up, everything flared very, very bright…

And the Replicators were gone, dissolved into piles of components.

Alice peered down at one of the heaps, frowning. "That's lovely, Replicator parts all over me," she muttered.

John ignored her. "Good old Plan D – works every time. You guys stay here a sec." He headed out of the cell, followed by Ronon. Behind him he could vaguely hear Jack explaining the plan to Woolsey.

The corridor was empty, bar two more piles of Replicator at various points. John nodded, glancing at Ronon. "Looks like we're clear. Go round 'em up…we need to head off _Daedalus_ before she attacks us." Ronon nodded, turning to go back to the cell.

"Where've you been?" John murmured.

Alice looked up from the second pile of parts. "Don't go in the brig."

"Yes. We've been running around the City for a while, now."

"I had things to do," she said vaguely. "You're clear of Asurans, but your ship is about ready to attack."

Elizabeth and the others reappeared, pouring past John and heading for the nearest transporter. Jack was behind them, pausing by John. "Coming?"

"Yes sir," John said automatically.

"Didn't see much of your girl."

"She doesn't like the brig much. Some programming thing."

"Huh. She's a little odd."

"Yeah. You get used to her."

"Sheppard!" Rodney yelled from the transporter. "I think we'd all prefer _not_ to be blown up by our own side, since the Replicators failed so utterly, so if you wouldn't mind?"

***

The Replicators were creepy, but they could build. The Control Tower was already back in place, an almost perfect replica. Alice had – somewhat sulkily, and John really couldn't figure out what she was mad about – confirmed that the computers and databanks were up and running again, too.

Elizabeth was standing in her office, staring blankly at one of the walls. Jack tapped on the doorframe without stepping in. "Gettin' all settled in?"

"Easily – although their decorating? Little bit spartan for my liking." She came to join him, gazing towards the 'Gate. "But the Replicators did do a fine job on rebuilding Stargate Operations back to its original state. How about yourself? Do you check out OK?"

"Apparently I don't have any little tiny robots floating in my bloodstream, which is always nice to hear."

"Huh! That it is. So what now?"

"Oh, a Jumper ride home to the SGC, followed by a hot shower, followed by a hot toddy, followed by ..."

"I was thinking a little more selfishly," Elizabeth confessed. "What are the chances of my team staying here in Atlantis?"

"Elizabeth, if it were up to me ..."

"It _is_ up to you," she pointed out quickly.

"... Right," he agreed slowly.

"John Sheppard is my captain," Alice added from behind him. "This City wants no one else."

"You can stay," Jack agreed.

"Really?" Elizabeth asked.

"You're probably still gonna have to get the rubber stamp from the IOA, but since you saved Woolsey's ass and you did a fair job on mine, I don't think that'll be a problem."

"Well, I think I speak for all of us when I say thank you very much."

"Hey, you came back to rescue _me,_" Jack said easily.

"Hmm! Yes, we did."

"Of course, next time, consider bringing Carter with you."

Elizabeth smiled and he returned it, turning away.

"Welcome home," he added.

Elizabeth caught his arm before he could move past her, tugging him into a hug. Jack, slightly confused, carefully patted her on the back. She let go, smiling, and he turned away.

John was wandering the corridors nearby. Alice obligingly directed Jack to him, falling into step six feet behind them.

"I guess you already know the good news, huh?"

John nodded. "We're staying."

"You're staying. Did you know your city just threatened me?"

"She'll do that. The Alices like me. The Ryans, not so much."

"Ryans?"

"_Aurora_-class ships have AIs that manifest as males. Ryan. Cityships, 'Jumpers and some research posts have Alices. The Alices tend to like me better than the Ryans do."

"She's loyal to you."

"Yes."

"Not the expedition. Not Earth, or humans. Just you." Jack glanced over his shoulder; Alice was gone.

"She's loyal to the Ancients. I'm…a stand in. A surrogate." John didn't bother following his gaze. "She's not listening."

"You haven't told anyone?"

"Teyla. Lorne. Radek." He thought for a minute. "And I'm getting suspicious of Carson, but I haven't actually told him."

"Radek, but not Rodney?"

"It'd just annoy Rodney. He can't see her, or hear her. Radek knows how to work with them…he and Ryan saved the i_Orion_/i, during the fight with Michael."

"The Antarctic base have an Alice?"

"I don't know. She needs a lot of power to be effective, so she's probably not online even if she's there." Glancing around, he added "Alice?"

"Yes, John."

"The base in Antarctica, does it have an Alice?"

"No. It's a weapons post, not research. There's no need for an Alice there." She glanced at Jack. "We can arrange a program, if the power's there to run it, but she'll have no function. There's nothing there we can affect."

"Seems a little pointless, then," Jack said thoughtfully.

"We're entertaining to talk to."

"She's entertained by talking down to us," John corrected her. "Sir, does…"

"She doesn't need to be in the report," Jack said when he trailed off. "I'll talk to Woolsey." He eyed John. "They'll find out, eventually."

"Yeah." He glanced at Alice, waiting patiently for an order. "Radek figured it out. And if Carson knows, he figured it out as well. Teyla, too."

"Lorne heard me," Alice offered. "General O'Neill is the only person who saw me first, except you."

"None of the others _can_ see you," John pointed out.

"Not the point. You haven't told anyone about me cold, yet. They've all known. General O'Neill's told more people than you have."

"I told one person!" Jack protested. "Because he was standing right there."

"One is more than none," she pointed out.

"Yeah, you're not going to win," John drawled. "She's very particular."

"You're sure she's never met Carter?"

"Pretty sure."

"Who's Carter?"


	22. Sunday

3.14 – Sunday

John stood near the door of the pier, watching Rodney stare out to sea from the far end. The funeral had been awful; Mrs Beckett had thanked them quietly for bringing Carson home, and then, without any fuss, fallen to her knees and cried. One of the cousins had come to help Elizabeth with her and the rest of the Atlantis crew had been left to make increasingly awkward small talk.

"Alice," John said quietly. She'd stayed away during the whole crisis, turning up only during the memorial just before their return to Earth.

"Yes, John," she said quietly from behind him. He turned to glance at her; she was a little subdued, but with the exception of a black band around one arm she looked perfectly normal.

"Is Rodney ok?"

"He's talking to himself."

"He always talks to himself."

"It's not about anyone's incompetence."

John grimaced. "That might be a problem."

"He feels guilty," Alice noted.

"We all feel guilty. Heightmeyer's going to be busy for a while."

"I like her. She's very nice."

"Someone actually thought this thing was a good idea?" John demanded, suddenly angry. "Explosive tumours? How was it..."

"It was considered a good way to inflict extra damage. Someone infected could potentially travel quite a long distance and take many others with them." She blinked at his glare. "It was abandoned, John, early. That's why it took so long for me to remember what it was, what it did. I got the information to Rodney as quickly as I could. I promise."

"You're supposed to warn me about things like this," John murmured, but the anger was gone.

"I don't remember everything. Things like that...that are so old...they're not in my primary memory. I have to go look. Sometimes it takes time. I'm truly sorry."

"Is that necessary?" he asked, gesturing to the band. "No one's going to see it."

"I liked Carson. He was a good man. It's about the only thing I can do for him." She tugged at the band. "I'll take it off if you want."

"No. Whatever." John looked back out towards Rodney; he seemed to be done talking and was just staring, shoulders hunched. "Did Carson know about you?" he asked suddenly.

Alice didn't answer and he turned to look at her again. "Alice."

"No," she said finally.

"But?" John prodded, recognising the tone.

"He didn't know about me," Alice repeated carefully. "But he knew...he knew this wasn't just a city. Not just buildings. Sometimes he talked to us, to himself, to me. Just to pass time, or to hear himself. He knew you knew and he didn't want to. He never asked anything. He just talked."

"But he heard you? He'd have seen you, if you wanted?"

"If he wanted," she corrected him. "He didn't want to know about me. I did my best to honour that. Sometimes he heard me speak with you. He tried not to listen. Like eavesdropping, he said once."

John nodded slowly, glancing out along the pier. Rodney had given up and was wandering back towards them. "You should have told me."

"Nothing to tell. 'Good morning, John, Carson doesn't know about me.' "

"That's..." He lowered his voice as Rodney glanced up. "A matter of opinion," he finished. "Go and scan something."

"Yes, John," Alice agreed. She paused to add, "I'm sorry. I'll miss him."

"You and everyone else," John breathed, turning to meet Rodney as he reached the door.


	23. Chapter 23

Author's note: This is an experiment in a new style for one chapter; events from Alice's POV. I just thought it'd be cool. I'm putting up a snippet to gauge peoples' reactions; if y'all hate it, I'll do the chapter as normal. Let me know what you think.

SUBMERSION

_Hull stress nominal. Readout sent to HUD for Captain's consideration. Current ahead, warnings to HUD._

_Query from TeylaEmmagen to CaptainJohnSheppard:_ Are we alone?

_Response from CaptainJohnSheppard:_ No.

_Attention paid to avatar, indicates desire for discussion._

_Query from TeylaEmmagen to avatar: _Alice, are you in contact with the station?

_Voice analysis suggests discomfort. Discomfort previously noted after missions greater than four hours. Suggest reason: claustrophobia exacerbated by length of mission. Suggest treatment: distraction or exit. Exit currently unavailable._

_Contact ping, mobile drilling platform: no response. Distance, greater than optimal transfer range. _

_Sensors indicate unstable rock formation. Suggested revised course sent to HUD for Captain's consideration._

_Contact ping, mobile drilling platform: no response._

_Response to TeylaEmmagen: _We're too far away.

_Clarification from CaptainJohnSheppard to TeylaEmmagen: _We're too far away. Water makes it harder. She has problems getting the signal through.

_Query from TeylaEmmagen: _Is there an Alice on the station?

_CaptainJohnSheppard_: There's a Ryan, but she thinks he's offline. There's not much power left. OK, kids. Do I have to pull this thing over? It's hard enough being in this damned thing for hours without listening to you guys.

_ScienceHeadRodneyMcKay talking with team member. As normal._

_CaptainJohnSheppard to CommanderElizabethWeir: _Well, still glad you came?

_CommanderElizabethWeir: (Voice analysis indicates sarcasm)_ Oh, sorry. I was preoccupied thinking about the geothermal drilling platform.

_CaptainJohnSheppard_: Shouldn't take us much longer. We just passed the thermal layer and I'm getting some readings a couple of hundred feet ahead.

_Contact ping, mobile drilling station. Contact. Information to HUD for Captain's perusal._

_CaptainJohnSheppard to team:_ OK, kids, we're here.

_Information to CaptainJohnSheppard:_ The AI is offline. There's power there, but it's powered down.

_CaptainJohnSheppard_: Well, hopefully it won't take too much longer to power up the station.

_Comment to CaptainJohnSheppard: _Not when it senses you.

_Contact ping. Power returning to Mobile Drilling Station. Lights powering on, systems powering up. Sensors, partial success. Internal lights, life support, 100%._


End file.
